Compositions and methods for characterizing marker dna from a sample

ABSTRACT

Provided herein is technology relating compositions and methods for detecting tissue cell-specific DNA, such as epithelial cell-specific DNA, in blood or blood products from a subject. The technology also relates to use of tissue cell-specific DNAs as internal controls for methylation assays.

The present application is a continuation from U.S. patent applicationSer. No. 16/665,731, filed Oct. 28, 2019, which is a divisional of U.S.patent application Ser. No. 14/966,617, filed Dec. 11, 2015, now U.S.Pat. No. 10,465,248, which claims priority to U.S. ProvisionalApplication Ser. No. 62/091,069, filed Dec. 12, 2014, each of which isincorporated herein by reference.

SEQUENCE LISTING

The text of the computer readable sequence listing filed herewith,titled “34706-303_SEQUENCE_LISTING_ST25”, created Feb. 25, 2020, havinga file size of 12,000 bytes, is hereby incorporated by reference in itsentirety.

FIELD OF INVENTION

Provided herein is technology relating compositions and methods fordetecting epithelial cell-specific DNA in blood or blood products from asubject, wherein the presence and amount of the epithelial cell DNA inthe blood or blood product is indicative of the presence of or themagnitude of a medical condition in the subject. The technology furtherrelates to use of tissue cell-specific DNAs, e.g., epithelialcell-specific DNA, as internal controls for methylation assays insamples such as stool or tissue samples from a subject.

BACKGROUND

Methylated DNA has been studied as a potential class of biomarkers inthe tissues of most tumor types. In many instances, DNAmethyltransferases add a methyl group to DNA atcytosine-phosphate-guanine (CpG) island sites as an epigenetic controlof gene expression. In a biologically attractive mechanism, acquiredmethylation events in promoter regions of tumor suppressor genes arethought to silence expression, thus contributing to oncogenesis. DNAmethylation may be a more chemically and biologically stable diagnostictool than RNA or protein expression (Laird (2010) “Principles andchallenges of genome-wide DNA methylation analysis” Nat Rev Genet 11:191-203). Furthermore, in other cancers like sporadic colon cancer,methylation markers offer excellent specificity and are more broadlyinformative and sensitive than are individual DNA mutations (Zou et al(2007) “Highly methylated genes in colorectal neoplasia: implicationsfor screening” Cancer Epidemiol Biomarkers Prev 16: 2686-96).

Nucleic acids from patient samples, e.g., blood, stool, and tissuesamples, that are analyzed for the presence of mutations and/or formethylation status associated with disease or risk of disease typicallypass through a number of process steps during analysis. These steps maycomprise, e.g., filtration, precipitation, capture, washing, elution,and/or chemical modification. For analysis of DNAs to determinemethylation status, e.g., the percent methylation of a test DNA,processing typically comprises treatment with bisulfite to convertun-methylated dC bases to dU residues, making them more readilydistinguishable from the methyl-C residues that are protected frombisulfite conversion.

Accurate quantitation of a test DNA (e.g., determining percentmethylation, presence and amount of DNA carrying a mutation, etc.)typically requires normalization to a control nucleic acid, e.g., anendogenous invariant gene having known features (e.g., known sequence,known copy-number per cell). Normalizing controls for sample-to-samplevariations that may occur in, for example, sample processing, assayefficiency, etc., and allows accurate sample-to-sample data comparison.

Cancer-specific marker DNA in blood or blood products, present eitherwithin circulating cancer cells or complexes, or as circulatingcell-free DNA, has been used for characterizing solid tumors, e.g.,breast carcinomas, in subjects. However, the utility of analyzing bloodfor particular cancer markers is limited to the assessment of particularsource tumors or types of cancers that have already been characterizedfor those markers, and the detection of particular markers in a theblood of a subject may be of limited use in detecting other conditionsor cancers.

SUMMARY

Provided herein is technology relating to characterizing samples, e.g.,blood samples, stool samples, etc., for the presence or absence of,and/or the amounts of different species of nucleic acids that, forexample, may be associated with a health status of a subject. Forexample, in some embodiments, the technology relates to detecting andmeasuring DNA associated with a particular tissue in a sample type thatdoes not typically contain DNA from that tissue. In preferredembodiments, the technology is directed to detecting and/or measuringepithelial cells and/or epithelial cell-specific DNA in blood or bloodproduct samples.

In some embodiments, the technology provides a method for monitoring adisease state in a subject, the method comprising the steps of, forexample, obtaining a first blood product sample from a subject at afirst time point; initiating a treatment protocol, where the treatmentprotocol comprises therapeutic intervention; obtaining a second bloodproduct sample from the subject at a second time point, wherein thesecond time point is after initiation of said treatment protocol; andassaying the first blood product sample and the second blood productsample for an amount of an epithelial cell-specific DNA, wherein adifference in the amount of epithelial cell-specific DNA between thefirst blood product sample and the second blood product sample isindicative of a change in the disease state in said subject. Thetechnology is not limited with respect to when the first and secondblood product samples are assayed. For example, in some embodiments, thefirst blood product sample is assayed before the start of the treatmentprotocol, while in other embodiments, the first blood product sample isassayed during the treatment protocol, or after the treatment protocol,e.g., at the same time as the second blood product sample. In preferredembodiments, the method comprises generating a record, e.g., a patientrecord such a hard-copy or electronic medical record, wherein the recordreports a result of the assaying, e.g., reports a value (e.g., anamount, or change in amount of epithelial call-specific DNA incomparative samples), or a diagnostic result that is based on a value.

The methods are not limited to any particular treatment protocol. Insome embodiments, the treatment protocol may comprise no activeintervention, e.g., it may be a matter of keeping a subject underobservation. In preferred embodiments, the treatment protocol comprisesone or more of surgery, drug therapy, chemotherapy, immunotherapy,nutritional therapy, radiation therapy, temperature therapy, andphysical therapy.

A difference in the amount of epithelial cell-specific DNA between thefirst blood product sample and the second blood product sample isindicative, for example, of recurrence, progression, or regression ofthe disease state in said subject. In some embodiments, no treatmentprotocol is used after the first sample is collected, and a differencein the amount of epithelial cell-specific DNA between the first bloodproduct sample and the second blood product sample is indicative of aninitial occurrence of a disease state in the subject. In someembodiments, the disease state indicated by the presence of epithelialcell-specific DNA in blood or a blood product sample is cancer, e.g.,metastatic cancer.

In some preferred embodiments, the epithelial cell-specific DNAcomprises a DNA that is methylated in epithelial cells and is notmethylated in blood cells. In such embodiments, a preferred methodcomprises treating DNA from the blood product sample(s) with a bisulfitereagent to create converted epithelial cell-specific DNA. In preferredembodiments, the epithelial cell-specific DNA comprises ZDHHC1 DNA, andin particularly preferred embodiments, the DNA comprises at least aportion of the sequence shown in SEQ ID NO:26.

The method is not limited to any particular form of blood or bloodproduct sample, In certain preferred embodiments, the blood product isplasma.

The methods are not limited to any particular means of assaying thesamples. In certain preferred embodiments, assaying comprises usingpolymerase chain reaction, nucleic acid sequencing, mass spectrometry,methylation-specific nuclease, mass-based separation, or DNA targetcapture. In particularly preferred embodiments, assaying comprises usinga flap endonuclease assay.

In some embodiments, the technology provides compositions related toanalyzing sample(s) from a subject. For example, in some embodiments,the composition comprises a strand of DNA comprising the nucleotidesequence of SEQ ID NO:33, and/or a strand of DNA comprising thenucleotide sequence of SEQ ID NO:27. In some embodiments, thecomposition further comprising a detection probe oligonucleotide,wherein the detection probe oligonucleotide comprises a region that iscomplementary to a portion of said strand of DNA. In preferredembodiments, the detection probe oligonucleotide comprises a region thatis complementary to a portion of SEQ ID NO:27 and/or to a portion of SEQID NO:33. In particularly preferred embodiments, the detection probeoligonucleotide comprises a reporter molecule. The reporter molecule isnot limited to any particular detectable moiety. In preferredembodiments, the reporter molecule comprises a fluorophore. In someembodiments, the detection probe comprises a flap sequence.

In certain preferred embodiments, the composition further comprises oneor more of a FRET cassette oligonucleotide, flap endonuclease, e.g., aFEN-1 endonuclease, and/or a DNA polymerase, e.g., a thermostable DNApolymerase. In preferred embodiments, the DNA polymerase is a bacterialDNA polymerase. In some embodiments, the technology provides a reactionmixture, e.g., for a detection assay, comprising any combination of thecompositions described above.

In some embodiments, the technology relates to performing methylationassays. In particular, in some embodiments, the technology relates tointernal controls for methylation assays.

In some embodiments, the technology provides a method of characterizinga blood or blood product sample from a subject comprising assaying saidsample to detect the presence of tissue cell-specific DNA, wherein thepresence of the tissue cell-specific DNA is indicative of the presenceof tissue cells or DNA from tissue cells in the blood or blood productsample. Tissue cell DNA may be present within tissue cells in the blood,or within other complexes (e.g., nucleosomes, episomes, immunecomplexes, microparticles, etc., or it may be in the form of circulatingcell-free DNA (ccfDNA). In some embodiments, the tissue cell-specificDNA is epithelial cell-specific DNA. In certain preferred embodiments,the blood product sample is a plasma sample.

In some particularly preferred embodiments, the tissue cell-specific DNAis epithelial cell-specific DNA that is methylated in epithelial cellsand is not methylated in blood cells, and the application of thetechnology preferably comprises treating DNA from the sample with abisulfite reagent to create converted tissue cell-specific DNA. Inparticularly preferred embodiments, the epithelial cell-specific DNAcomprises ZDHHC1 DNA, as described herein below.

The method of analyzing the tissue-cell specific DNA is not limited toany particular method of DNA analysis. In come embodiments, the assayingcomprises using polymerase chain reaction, nucleic acid sequencing, massspectrometry, methylation-specific nuclease, mass-based separation,and/or DNA target capture. In preferred embodiments, the assay comprisesa flap endonuclease assay. In some preferred embodiments, the assay is aflap endonuclease assay, e.g., a QUARTS assay.

In some embodiments, the technology provides reference DNAs that areusable for determining total human DNA input in a sample, as a means ofdetermining the relative amount of a test nucleic acid, e.g., thepercentage of methylation of a cancer marker gene, in the sample. Incertain preferred embodiments, the technology provides reference DNAshaving methylation features similar to the marker DNAs to which they areto be compared, such that the reference DNAs can be exposed to the samepreparative steps as marker DNAs, and will behave like marker DNAs.

In some embodiments, the technology provides control or marker DNAs thatare specific for tissue cells, e.g., epithelial cells. In particularembodiments, the technology provides marker DNAs that are highlymethylated, e.g., in tissue cells, —e.g., both normal and cancerepithelial cells—but that are not methylated in blood, e.g., inlymphocytes. These marker DNAs find numerous applications. For example,in some embodiments, these markers find use as control or reference DNAsin quantifying tissue-derived DNA in samples that may also contain bloodcells such as lymphocytes that would produce background in the detectionof other control DNAs, e.g., β-actin. These tissue cell-specific markersalso find application in the detection of tissue cells in samples wheretissue cells or tissue DNA are normally absent, e.g., in blood, whereinthe presence of tissue cells or tissue DNA may indicate the presence ofdisease, e.g., metastasis in cancer.

For example, in some embodiments, the technology provides methods ofperforming a quantitative nucleic acid detection assay, comprisingassaying a sample from a subject for an amount of at least one markergene; assaying the same sample for an amount of ZDHHC1 DNA, andcomparing the amount of the at least one marker gene to the amount ofZDHHC1 DNA in the sample to determine the amount of the at least onemarker gene relative to the amount of ZDHHC1 DNA in said sample. In someembodiments, external controls, e.g., calibration standards may be usedto determine absolute quantitation of the marker genes and/or the ZDHHC1DNA.

In some embodiments, the technology comprises treating DNA from thesample with a bisulfite reagent to create converted ZDHHC1 DNA and atleast one converted marker gene, such that assaying for an amount of amarker gene and the ZDHHC1 DNA comprises assaying an amount of convertedmarker gene and converted ZDHHC1 DNA.

The methods of assaying the nucleic acids recited above are not limitedto any particular method. In some embodiments, the assaying comprisesusing one or more of polymerase chain reaction, nucleic acid sequencing,mass spectrometry, methylation specific nuclease, mass-based separation,or target capture. In some preferred embodiments, assaying of the markerDNA and assaying of the ZDHHC1 DNA are done in a single reaction. Inparticularly preferred embodiments, the assay is a flap endonucleaseassay, e.g., a QUARTS assay.

In some embodiments, the amount of converted marker gene relative to theamount of converted ZDHHC1 DNA is indicative of a methylation state ofthe marker, e.g., in a test sample, and the methylation state comprisesincreased or decreased methylation of the marker gene relative to anormal methylation state of the marker gene. In certain preferredembodiments, an increased percent methylation is indicative of a diseasestate.

Further embodiments provide a method of detecting tissue cells in bloodor blood product, comprising: detecting the presence of methylatedZDHHC1 in a blood or blood product sample from a subject, wherein thepresence of the methylated ZDHHC1 is indicative of the presence oftissue cells, e.g., epithelial cells, in the blood. In some embodiments,the presence of tissue cells in the sample is indicative of metastaticcancer in the subject. In some embodiments, the blood product is plasma.In some embodiments, the assaying comprises using polymerase chainreaction, nucleic acid sequencing, mass spectrometry, methylationspecific nuclease, mass-based separation, or target capture. In someembodiments, the assay is a flap endonuclease assay, e.g., a QUARTSassay. In some embodiments, the cancer is colorectal cancer.

Additional embodiments provide a method of detecting metastatic cancerin a blood or blood product sample from a subject, comprising: detectingthe presence of methylated ZDHHC1 in a blood or blood product samplefrom a subject, wherein the presence of the methylated ZDHHC1 isindicative of the presence of metastatic cancer in the subject.

Yet other embodiments provide a kit, comprising: a) at least oneoligonucleotide, wherein at least a portion of the oligonucleotidespecifically hybridizes to ZDHHC1; and b) bisulfite. In someembodiments, the oligonucleotide is selected from one or more of, forexample, a capture oligonucleotide, a pair of nucleic acid primers, anucleic acid probe, or an INVADER oligonucleotide. In some embodiments,the kit further comprises one or more nucleic acids that specificallyhybridize to one or more target genes. In some embodiments, the kitfurther comprises a solid support (e.g. magnetic bead). In someembodiments, the solid support comprises one or more capture reagents(e.g., oligonucleotides complementary to ZDHHC1 and/or additional targetgenes).

Additional embodiments provide a composition, comprising: a complex of aZDHHC1 nucleic acid and at least one oligonucleotide, wherein at least aportion of the oligonucleotide is hybridized to the ZDHHC1 nucleic acid.In some embodiments, the compositions further comprises one or moreadditional reaction mixtures comprising a complex of a target nucleicacid and one or more oligonucleotides that specifically hybridize to oneor more target genes.

Still further embodiments provide a method of screening for a neoplasmin a sample obtained from a subject, the method comprising: a) assayinga sample from a subject for an amount of at least one methylated markergene selected from the group consisting of vimentin, septin 9, NDRG4,and BMP3 in a sample obtained from a subject; assaying the sample for anamount of methylated ZDHHC1 DNA, and comparing the amount of the atleast one methylated marker gene to the amount of methylated ZDHHC1 DNAin the sample to determine a methylation state for the at least onemarker gene in the sample In some embodiments, the at least one markeris at least two, three, four, or all of the markers. In someembodiments, the assay further comprises the step of identifying a KRASmutation score in the sample. In some embodiments, measuring of theK-ras mutation score is measured by quantitative allele-specific PCR. Insome embodiments, the assay comprises detecting methylation states ofZDHHC1, BMP3, NDRG4, and identifying a KRAS mutation score in thesample. In some embodiments, the method further comprises the step ofdetermining the presence of hemoglobin in the sample.

In some embodiments, the patient has inflammatory bowel disease. Incertain preferred embodiments, the sample is a stool sample, a tissuesample, a pancreatic juice sample, a pancreatic cyst fluid sample, ablood sample, or a urine sample. A neoplasm may comprise, for example, apancreas neoplasm, a colorectal neoplasm, a bile duct neoplasm, astomach neoplasm, an esophagus neoplasm, or an adenoma.

Some embodiments provide a kit, comprising: a) at least oneoligonucleotide, wherein at least a portion of the oligonucleotidespecifically hybridizes to ZDHHC1; and b) at least one additionaloligonucleotide, wherein at least a portion of the oligonucleotidespecifically hybridizes to marker selected from vimentin, septin 9,NDRG4, and BMP3. In some embodiments, the kit comprises at least twoadditional oligonucleotides. In some embodiments, the kit furthercomprises bisulfite. In some embodiments, the kit further comprises atleast one oligonucleotide, wherein at least a portion of theoligonucleotide specifically hybridizes to KRAS. In some embodiments,the kit further comprises reagents for detecting the presence ofhemoglobin in a stool sample.

Certain embodiments provide a composition, comprising: a) a complex of aZDHHC1 nucleic acid and at least one oligonucleotide, wherein at least aportion of the oligonucleotide is hybridized to the ZDHHC1 nucleic acid;and b) a complex of a target nucleic acid selected from the groupconsisting of vimentin, septin 9, NDRG4, and BMP, and one or moreoligonucleotides that specifically hybridize to the target nucleic acid.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the presenttechnology will become better understood with regard to the followingdrawings:

FIGS. 1A-1E provide graphs comparing the presence of β-actin (BTACT) andthe methylated gene ZDHHC1 in bisulfite-converted DNA from stool, blood,cell lines, and tissue samples.

FIGS. 2A-2C provide graphs comparing the % methylation of marker geneNDRG4 as determined by comparison to control genes BTACT or ZDHHC1measured in stool samples (2A), cell lines (2B) and colorectal cancertissues samples (2C).

FIGS. 3A-3C provide graphs comparing the % methylation of marker geneBMP3 determined by comparison to control genes BTACT or ZDHHC1 in stoolsamples (3A), cell lines (3B) and colorectal cancer tissues samples(3C).

FIGS. 4A-4E provides a table showing the detection of the levels of theZDHHC1 marker in plasma samples from subjects having the indicatedcancers and from normal subjects.

DEFINITIONS

To facilitate an understanding of the present technology, a number ofterms and phrases are defined below. Additional definitions are setforth throughout the detailed description.

As used herein, “a” or “an” or “the” can mean one or more than one. Forexample, “a” widget can mean one widget or a plurality of widgets.

As used herein, the terms “subject” and “patient” refer to any animal,such as a dog, cat, bird, livestock, and particularly a mammal,preferably a human. In some instances, the subject is also a “user” (andthus the user is also the subject or patient).

As used herein, the term “sample” and “specimen” are usedinterchangeably, and in the broadest senses. In one sense, sample ismeant to include a specimen or culture obtained from any source, as wellas biological and environmental samples. Biological samples may beobtained from animals (including humans) and encompass fluids, solids,tissues, and gases. Biological samples include blood products, such asplasma, serum, stool, urine, and the like. Environmental samples includeenvironmental material such as surface matter, soil, mud, sludge,biofilms, water, crystals, and industrial samples. Such examples are nothowever to be construed as limiting the sample types applicable to thepresent invention.

As used herein, a “remote sample” as used in some contexts relates to asample indirectly collected from a site that is not the cell, tissue, ororgan source of the sample. For instance, when sample materialoriginating from the pancreas is assessed in a stool sample (e.g., notfrom a sample taken directly from a pancreas), the sample is a remotesample.

The term “target,” when used in reference to a nucleic acid capture,detection, or analysis method, generally refers to a nucleic acid havinga feature, e.g., a particular sequence of nucleotides to be detected oranalyzed, e.g., in a sample suspected of containing the target nucleicacid. In some embodiments, a target is a nucleic acid having aparticular sequence for which it is desirable to determine a methylationstatus. When used in reference to the polymerase chain reaction,“target” generally refers to the region of nucleic acid bounded by theprimers used for polymerase chain reaction. Thus, the “target” is soughtto be sorted out from other nucleic acid sequences that may be presentin a sample. A “segment” is defined as a region of nucleic acid withinthe target sequence. The term “sample template” refers to nucleic acidoriginating from a sample that is analyzed for the presence of a target.

As used herein, the term “locus” refers to a particular position, e.g.,of a mutation, polymorphism, or a C residue in a CpG dinucleotide,within a defined region or segment of nucleic acid, such as a gene orany other characterized sequence on a chromosome or RNA molecule. Alocus is not limited to any particular size or length, and may refer toa portion of a chromosome, a gene, functional genetic element, or asingle nucleotide or base pair. As used herein in reference to CpG sitesthat may be methylated, a locus refers to the C residue in the CpGdinucleotide.

As used herein, “a capture reagent” refers to any agent that is capableof binding to an analyte (e.g., a target). Preferably, “a capturereagent” refers to any agent that is capable of specifically binding toan analyte, e.g., having a higher binding affinity and/or specificity tothe analyte than to any other moiety. Any moiety, such as a cell, acellular organelle, an inorganic molecule, an organic molecule and amixture or complex thereof can be used as a capture reagent if it hasthe requisite binding affinity and/or specificity to the analyte. Thecapture reagents can be peptides, proteins, e.g., antibodies orreceptors, oligonucleotides, nucleic acids, vitamins, oligosaccharides,carbohydrates, lipids, small molecules, or a complex thereof. Capturereagents that comprise nucleic acids, e.g., oligonucleotides, maycapture a nucleic acid target by sequence-specific hybridization (e.g.,through the formation of conventional Watson-Crick basepairs), orthrough other binding interactions. When a capture oligonucleotidehybridizes to a target nucleic acid, hybridization may involve a portionof the oligonucleotide, or the complete oligonucleotide sequence, andthe oligonucleotide may bind to a portion of or to the complete targetnucleic acid sequence.

The term “amplifying” or “amplification” in the context of nucleic acidsrefers to the production of multiple copies of a polynucleotide, or aportion of the polynucleotide, typically starting from a small amount ofthe polynucleotide (e.g., a single polynucleotide molecule), where theamplification products or amplicons are generally detectable.Amplification of polynucleotides encompasses a variety of chemical andenzymatic processes. The generation of multiple DNA copies from one or afew copies of a target or template DNA molecule during a polymerasechain reaction (PCR) or a ligase chain reaction (LCR; see, e.g., U.S.Pat. No. 5,494,810; herein incorporated by reference in its entirety)are forms of amplification. Additional types of amplification include,but are not limited to, allele-specific PCR (see, e.g., U.S. Pat. No.5,639,611; herein incorporated by reference in its entirety), assemblyPCR (see, e.g., U.S. Pat. No. 5,965,408; herein incorporated byreference in its entirety), helicase-dependent amplification (see, e.g.,U.S. Pat. No. 7,662,594; herein incorporated by reference in itsentirety), hot-start PCR (see, e.g., U.S. Pat. Nos. 5,773,258 and5,338,671; each herein incorporated by reference in their entireties),intersequence-specific PCR, inverse PCR (see, e.g., Triglia, et al.(1988) Nucleic Acids Res., 16:8186; herein incorporated by reference inits entirety), ligation-mediated PCR (see, e.g., Guilfoyle, R. et al.,Nucleic Acids Research, 25:1854-1858 (1997); U.S. Pat. No. 5,508,169;each of which are herein incorporated by reference in their entireties),methylation-specific PCR (see, e.g., Herman, et al., (1996) PNAS 93(13)9821-9826; herein incorporated by reference in its entirety), miniprimerPCR, multiplex ligation-dependent probe amplification (see, e.g.,Schouten, et al., (2002) Nucleic Acids Research 30(12): e57; hereinincorporated by reference in its entirety), multiplex PCR (see, e.g.,Chamberlain, et al., (1988) Nucleic Acids Research 16(23) 11141-11156;Ballabio, et al., (1990) Human Genetics 84(6) 571-573; Hayden, et al.,(2008) BMC Genetics 9:80; each of which are herein incorporated byreference in their entireties), nested PCR, overlap-extension PCR (see,e.g., Higuchi, et al., (1988) Nucleic Acids Research 16(15) 7351-7367;herein incorporated by reference in its entirety), real time PCR (see,e.g., Higuchi, et al., (1992) Biotechnology 10:413-417; Higuchi, et al.,(1993) Biotechnology 11:1026-1030; each of which are herein incorporatedby reference in their entireties), reverse transcription PCR (see, e.g.,Bustin, S. A. (2000) J. Molecular Endocrinology 25:169-193; hereinincorporated by reference in its entirety), solid phase PCR, thermalasymmetric interlaced PCR, and Touchdown PCR (see, e.g., Don, et al.,Nucleic Acids Research (1991) 19(14) 4008; Roux, K. (1994) Biotechniques16(5) 812-814; Hecker, et al., (1996) Biotechniques 20(3) 478-485; eachof which are herein incorporated by reference in their entireties).Polynucleotide amplification also can be accomplished using digital PCR(see, e.g., Kalinina, et al., Nucleic Acids Research. 25; 1999-2004,(1997); Vogelstein and Kinzler, Proc Natl Acad Sci USA. 96; 9236-41,(1999); International Patent Publication No. WO05023091A2; US PatentApplication Publication No. 20070202525; each of which are incorporatedherein by reference in their entireties).

The term “polymerase chain reaction” (“PCR”) refers to the method of K.B. Mullis U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,965,188, thatdescribe a method for increasing the concentration of a segment of atarget sequence in a mixture of genomic or other DNA or RNA, withoutcloning or purification. This process for amplifying the target sequenceconsists of introducing a large excess of two oligonucleotide primers tothe DNA mixture containing the desired target sequence, followed by aprecise sequence of thermal cycling in the presence of a DNA polymerase.The two primers are complementary to their respective strands of thedouble stranded target sequence. To effect amplification, the mixture isdenatured and the primers then annealed to their complementary sequenceswithin the target molecule. Following annealing, the primers areextended with a polymerase so as to form a new pair of complementarystrands. The steps of denaturation, primer annealing, and polymeraseextension can be repeated many times (i.e., denaturation, annealing andextension constitute one “cycle”; there can be numerous “cycles”) toobtain a high concentration of an amplified segment of the desiredtarget sequence. The length of the amplified segment of the desiredtarget sequence is determined by the relative positions of the primerswith respect to each other, and therefore, this length is a controllableparameter. By virtue of the repeating aspect of the process, the methodis referred to as the “polymerase chain reaction” (“PCR”). Because thedesired amplified segments of the target sequence become the predominantsequences (in terms of concentration) in the mixture, they are said tobe “PCR amplified” and are “PCR products” or “amplicons.” Those of skillin the art will understand the term “PCR” encompasses many variants ofthe originally described method using, e.g., real time PCR, nested PCR,reverse transcription PCR (RT-PCR), single primer and arbitrarily primedPCR, etc.

As used herein, the term “nucleic acid detection assay” refers to anymethod of determining the nucleotide composition of a nucleic acid ofinterest. Nucleic acid detection assay include but are not limited to,DNA sequencing methods, probe hybridization methods, structure specificcleavage assays (e.g., the INVADER assay, (Hologic, Inc.) and aredescribed, e.g., in U.S. Pat. Nos. 5,846,717, 5,985,557, 5,994,069,6,001,567, 6,090,543, and 6,872,816; Lyamichev et al., Nat. Biotech.,17:292 (1999), Hall et al., PNAS, USA, 97:8272 (2000), and US2009/0253142, each of which is herein incorporated by reference in itsentirety for all purposes); enzyme mismatch cleavage methods (e.g.,Variagenics, U.S. Pat. Nos. 6,110,684, 5,958,692, 5,851,770, hereinincorporated by reference in their entireties); polymerase chainreaction (PCR), described above; branched hybridization methods (e.g.,Chiron, U.S. Pat. Nos. 5,849,481, 5,710,264, 5,124,246, and 5,624,802,herein incorporated by reference in their entireties); rolling circlereplication (e.g., U.S. Pat. Nos. 6,210,884, 6,183,960 and 6,235,502,herein incorporated by reference in their entireties); NASBA (e.g., U.S.Pat. No. 5,409,818, herein incorporated by reference in its entirety);molecular beacon technology (e.g., U.S. Pat. No. 6,150,097, hereinincorporated by reference in its entirety); E-sensor technology(Motorola, U.S. Pat. Nos. 6,248,229, 6,221,583, 6,013,170, and6,063,573, herein incorporated by reference in their entireties);cycling probe technology (e.g., U.S. Pat. Nos. 5,403,711, 5,011,769, and5,660,988, herein incorporated by reference in their entireties); DadeBehring signal amplification methods (e.g., U.S. Pat. Nos. 6,121,001,6,110,677, 5,914,230, 5,882,867, and 5,792,614, herein incorporated byreference in their entireties); ligase chain reaction (e.g., BaranayProc. Natl. Acad. Sci USA 88, 189-93 (1991)); and sandwich hybridizationmethods (e.g., U.S. Pat. No. 5,288,609, herein incorporated by referencein its entirety).

In some embodiments, target nucleic acid is amplified (e.g., by PCR) andamplified nucleic acid is detected simultaneously using an invasivecleavage assay. Assays configured for performing a detection assay(e.g., invasive cleavage assay) in combination with an amplificationassay are described in US Patent Publication US 20090253142 A1(application Ser. No. 12/404,240), incorporated herein by reference inits entirety for all purposes. Additional amplification plus invasivecleavage detection configurations, termed the QuARTS method, aredescribed in U.S. Pat. Nos. 8,361,720; 8,715,937; 8,916,344; and9,127,318, incorporated herein by reference in their entireties for allpurposes. The term “invasive cleavage structure” as used herein refersto a cleavage structure comprising i) a target nucleic acid, ii) anupstream nucleic acid (e.g., an invasive or “INVADER” oligonucleotide),and iii) a downstream nucleic acid (e.g., a probe), where the upstreamand downstream nucleic acids anneal to contiguous regions of the targetnucleic acid, and where an overlap forms between the a 3′ portion of theupstream nucleic acid and duplex formed between the downstream nucleicacid and the target nucleic acid. An overlap occurs where one or morebases from the upstream and downstream nucleic acids occupy the sameposition with respect to a target nucleic acid base, whether or not theoverlapping base(s) of the upstream nucleic acid are complementary withthe target nucleic acid, and whether or not those bases are naturalbases or non-natural bases. In some embodiments, the 3′ portion of theupstream nucleic acid that overlaps with the downstream duplex is anon-base chemical moiety such as an aromatic ring structure, e.g., asdisclosed, for example, in U.S. Pat. No. 6,090,543, incorporated hereinby reference in its entirety. In some embodiments, one or more of thenucleic acids may be attached to each other, e.g., through a covalentlinkage such as nucleic acid stem-loop, or through a non-nucleic acidchemical linkage (e.g., a multi-carbon chain). As used herein, the term“flap endonuclease assay” includes “INVADER” invasive cleavage assaysand QuARTS assays, as described above.

As used herein, the terms “complementary” or “complementarity” used inreference to polynucleotides (i.e., a sequence of nucleotides) refers topolynucleotides related by the base-pairing rules. For example, thesequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.”Complementarity may be “partial,” in which only some of the nucleicacids' bases are matched according to the base pairing rules. Or, theremay be “complete” or “total” complementarity between the nucleic acids.The degree of complementarity between nucleic acid strands hassignificant effects on the efficiency and strength of hybridizationbetween nucleic acid strands. This is of particular importance inamplification reactions, as well as detection methods that depend uponbinding between nucleic acids.

As used herein, the term “primer” refers to an oligonucleotide, whetheroccurring naturally, as in a purified restriction digest, or producedsynthetically, that is capable of acting as a point of initiation ofsynthesis when placed under conditions in which synthesis of a primerextension product that is complementary to a nucleic acid strand isinduced (e.g., in the presence of nucleotides and an inducing agent suchas a biocatalyst (e.g., a DNA polymerase or the like). The primer istypically single stranded for maximum efficiency in amplification, butmay alternatively be partially or completely double stranded. Theportion of the primer that hybridizes to a template nucleic acid issufficiently long to prime the synthesis of extension products in thepresence of the inducing agent. The exact lengths of the primers willdepend on many factors, including temperature, source of primer and theuse of the method. Primers may comprise labels, tags, capture moieties,etc.

As used herein, the term “nucleic acid molecule” refers to any nucleicacid containing molecule, including but not limited to, DNA or RNA. Theterm encompasses sequences that include any of the known base analogs ofDNA and RNA including, but not limited to, 4 acetylcytosine,8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine,5-(carboxyhydroxyl-methyl) uracil, 5-fluorouracil, 5-bromouracil,5-carboxymethylaminomethyl-2-thiouracil,5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine,N6-isopentenyladenine, 1-methyladenine, 1-methylpseudo-uracil,1-methylguanine, 1-methylinosine, 2,2-dimethyl-guanine, 2-methyladenine,2-methylguanine, 3-methyl-cytosine, 5-methylcytosine, N6-methyladenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxy-amino-methyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarbonylmethyluracil, 5-methoxyuracil,2-methylthio-N-isopentenyladenine, uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine,2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,5-methyluracil, N-uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and2,6-diaminopurine.

As used herein, the term “nucleobase” is synonymous with other terms inuse in the art including “nucleotide,” “deoxynucleotide,” “nucleotideresidue,” “deoxynucleotide residue,” “nucleotide triphosphate (NTP),” ordeoxynucleotide triphosphate (dNTP).

An “oligonucleotide” refers to a nucleic acid that includes at least twonucleic acid monomer units (e.g., nucleotides), typically more thanthree monomer units, and more typically greater than ten monomer units.The exact size of an oligonucleotide generally depends on variousfactors, including the ultimate function or use of the oligonucleotide.To further illustrate, oligonucleotides are typically less than 200residues long (e.g., between 15 and 100), however, as used herein, theterm is also intended to encompass longer polynucleotide chains.Oligonucleotides are often referred to by their length. For example a 24residue oligonucleotide is referred to as a “24-mer”. Typically, thenucleoside monomers are linked by phosphodiester bonds or analogsthereof, including phosphorothioate, phosphorodithioate,phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,phosphoranilidate, phosphoramidate, and the like, including associatedcounterions, H⁺, NH₄ ⁺, Na⁺, and the like, if such counterions arepresent. Further, oligonucleotides are typically single-stranded.Oligonucleotides are optionally prepared by any suitable method,including, but not limited to, isolation of an existing or naturalsequence, DNA replication or amplification, reverse transcription,cloning and restriction digestion of appropriate sequences, or directchemical synthesis by a method such as the phosphotriester method ofNarang et al. (1979) Meth Enzymol. 68: 90-99; the phosphodiester methodof Brown et al. (1979) Meth Enzymol. 68: 109-151; thediethylphosphoramidite method of Beaucage et al. (1981) TetrahedronLett. 22: 1859-1862; the triester method of Matteucci et al. (1981) J AmChem Soc. 103:3185-3191; automated synthesis methods; or the solidsupport method of U.S. Pat. No. 4,458,066, entitled “PROCESS FORPREPARING POLYNUCLEOTIDES,” issued Jul. 3, 1984 to Caruthers et al., orother methods known to those skilled in the art. All of these referencesare incorporated by reference.

A “sequence” of a biopolymer refers to the order and identity of monomerunits (e.g., nucleotides, amino acids, etc.) in the biopolymer. Thesequence (e.g., base sequence) of a nucleic acid is typically read inthe 5′ to 3′ direction.

As used herein, the term “gene” refers to a nucleic acid (e.g., DNA)sequence that comprises coding sequences necessary for the production ofa polypeptide, precursor, or RNA (e.g., non-coding RNAs such asribosomal RNA, transfer RNA, splicosomal RNA, microRNA). A polypeptideor non-coding RNA can be encoded by a full length coding sequence or byany portion of the coding sequence so long as the desired activity orfunctional properties (e.g., enzymatic activity, ligand binding, signaltransduction, immunogenicity, etc.) of the full-length or fragmentpolypeptide are retained. The term also encompasses the coding region ofa structural gene and the sequences located adjacent to the codingregion on both the 5′ and 3′ ends for a distance of about 1 kb or moreon either end such that the gene corresponds to the length of thefull-length mRNA. Sequences located 5′ of the coding region and presenton the mRNA are referred to as 5′ non-translated sequences. Sequenceslocated 3′ or downstream of the coding region and present on the mRNAare referred to as 3′ non-translated sequences. The term “gene”encompasses both cDNA and genomic forms of a gene. A genomic form orclone of a gene contains the coding region interrupted with non-codingsequences termed “introns” or “intervening regions” or “interveningsequences.” Introns are segments of a gene that are transcribed intonuclear RNA (e.g., hnRNA); introns may contain regulatory elements(e.g., enhancers). Introns are removed or “spliced out” from the nuclearor primary transcript; introns therefore are absent in the messenger RNA(mRNA) transcript. The mRNA functions during translation to specify thesequence or order of amino acids in a nascent polypeptide.

In addition to containing introns, genomic forms of a gene may alsoinclude sequences located on both the 5′ and 3′ end of the sequencesthat are present on the RNA transcript. These sequences are referred toas “flanking” sequences or regions (these flanking sequences are located5′ or 3′ to the non-translated sequences present on the mRNAtranscript). The 5′ flanking region may contain regulatory sequencessuch as promoters and enhancers that control or influence thetranscription of the gene. The 3′ flanking region may contain sequencesthat direct the termination of transcription, post-transcriptionalcleavage and polyadenylation.

The term “wild-type” when made in reference to a gene refers to a genethat has the characteristics of a gene isolated from a naturallyoccurring source. The term “wild-type” when made in reference to a geneproduct refers to a gene product that has the characteristics of a geneproduct isolated from a naturally occurring source. The term“naturally-occurring” as applied to an object refers to the fact that anobject can be found in nature. For example, a polypeptide orpolynucleotide sequence that is present in an organism (includingviruses) that can be isolated from a source in nature and which has notbeen intentionally modified by the hand of a person in the laboratory isnaturally-occurring. A wild-type gene is often that gene or allele thatis most frequently observed in a population and is thus arbitrarilydesignated the “normal” or “wild-type” form of the gene. In contrast,the term “modified” or “mutant” when made in reference to a gene or to agene product refers, respectively, to a gene or to a gene product thatdisplays modifications in sequence and/or functional properties (e.g.,altered characteristics) when compared to the wild-type gene or geneproduct. It is noted that naturally-occurring mutants can be isolated;these are identified by the fact that they have altered characteristicswhen compared to the wild-type gene or gene product.

The term “allele” refers to a variation of a gene; the variationsinclude but are not limited to variants and mutants, polymorphic loci,and single nucleotide polymorphic loci, frameshift, and splicemutations. An allele may occur naturally in a population or it mightarise during the lifetime of any particular individual of thepopulation.

Thus, the terms “variant” and “mutant” when used in reference to anucleotide sequence refer to a nucleic acid sequence that differs by oneor more nucleotides from another, usually related, nucleotide acidsequence. A “variation” is a difference between two different nucleotidesequences; typically, one sequence is a reference sequence.

The term “solid support” as used herein includes all the materials onwhich a target (e.g., DNA) can be immobilized. Natural or syntheticmaterials, which may or may not be chemically modified, can be used as asolid support, in particular polymers such as polyvinyl chloride,polyethylene, polystyrenes, polyacrylate or polyamide, or copolymersbased on vinyl aromatic monomers, esters of unsaturated carboxylicacids, vinylidene chloride, dienes or compounds having nitrile functions(acrylonitrile); polymers of vinyl chloride and of propylene, polymersof vinyl chloride and vinyl acetate; copolymers based on styrenes orsubstituted derivatives of styrene; synthetic fibers, such as nylon;inorganic materials such as silica, glass, ceramic or quartz; latexes,magnetic particles; metal derivatives. Additional examples include, butare not limited to, a microtitration plate, a sheet, a cone, a tube, awell, beads (e.g., magnetic beads), particles or the like, or a flatsupport such as a silica or silicon wafer.

As used herein, the terms “magnetic particles” and “magnetic beads” areused interchangeably and refer to particles or beads that respond to amagnetic field. Typically, magnetic particles comprise materials thathave no magnetic field but that form a magnetic dipole when exposed to amagnetic field, e.g., materials capable of being magnetized in thepresence of a magnetic field but that are not themselves magnetic in theabsence of such a field. The term “magnetic” as used in this contextincludes materials that are paramagnetic or superparamagnetic materials.The term “magnetic”, as used herein, also encompasses temporarilymagnetic materials, such as ferromagnetic or ferrimagnetic materialswith low Curie temperatures, provided that such temporarily magneticmaterials are paramagnetic in the temperature range at which silicamagnetic particles containing such materials are used according to thepresent methods to isolate biological materials. The term “mixable” asused in reference to particles or beads refers to particles that are infree form, i.e., that are not immobilized, e.g., in a column, but thatcan be added to a sample and distributed in the sample fluid by mixingaction (e.g., vortexing, stirring, shaking, repeated pipetting, etc.).The term “probe” refers to an oligonucleotide (e.g., a sequence ofnucleotides), whether occurring naturally as in a purified restrictiondigest or produced synthetically, recombinantly, or by PCRamplification, that is capable of hybridizing to another oligonucleotideof interest. A probe may be single-stranded or double-stranded. Probesare useful in the detection, identification, and isolation of particulargene sequences (e.g., a “capture probe”). It is contemplated that anyprobe used in the present invention may, in some embodiments, be labeledwith any “reporter molecule,” so that is detectable in any detectionsystem, including, but not limited to enzyme (e.g., ELISA, as well asenzyme-based histochemical assays), fluorescent, radioactive, andluminescent systems. It is not intended that the present invention belimited to any particular detection system or label.

As used herein, “methylation” refers to cytosine methylation atpositions C5 or N4 of cytosine, the N6 position of adenine, or othertypes of nucleic acid methylation. In vitro amplified DNA is usuallyunmethylated because typical in vitro DNA amplification methods do notretain the methylation pattern of the amplification template. However,“unmethylated DNA” or “methylated DNA” can also refer to amplified DNAwhose original template was unmethylated or methylated, respectively.

Accordingly, as used herein a “methylated nucleotide” or a “methylatednucleotide base” refers to the presence of a methyl moiety on anucleotide base, where the methyl moiety is not present in a recognizedtypical nucleotide base. For example, cytosine does not contain a methylmoiety on its pyrimidine ring, but 5-methylcytosine contains a methylmoiety at position 5 of its pyrimidine ring. Therefore, cytosine is nota methylated nucleotide and 5-methylcytosine is a methylated nucleotide.In another example, thymine contains a methyl moiety at position 5 ofits pyrimidine ring; however, for purposes herein, thymine is notconsidered a methylated nucleotide when present in DNA since thymine isa typical nucleotide base of DNA.

As used herein, a “methylated nucleic acid molecule” refers to a nucleicacid molecule that contains one or more methylated nucleotides.

As used herein, a “methylation state”, “methylation profile”, and“methylation status” of a nucleic acid molecule refers to the presenceof absence of one or more methylated nucleotide bases in the nucleicacid molecule. For example, a nucleic acid molecule containing amethylated cytosine is considered methylated (e.g., the methylationstate of the nucleic acid molecule is methylated). A nucleic acidmolecule that does not contain any methylated nucleotides is consideredunmethylated.

The methylation state of a particular nucleic acid sequence (e.g., agene marker or DNA region as described herein) can indicate themethylation state of every base in the sequence or can indicate themethylation state of a subset of the bases (e.g., of one or morecytosines) within the sequence, or can indicate information regardingregional methylation density within the sequence with or withoutproviding precise information of the locations within the sequence themethylation occurs.

The methylation state of a nucleotide locus in a nucleic acid moleculerefers to the presence or absence of a methylated nucleotide at aparticular locus in the nucleic acid molecule. For example, themethylation state of a cytosine at the 7th nucleotide in a nucleic acidmolecule is methylated when the nucleotide present at the 7th nucleotidein the nucleic acid molecule is 5-methylcytosine. Similarly, themethylation state of a cytosine at the 7th nucleotide in a nucleic acidmolecule is unmethylated when the nucleotide present at the 7thnucleotide in the nucleic acid molecule is cytosine (and not5-methylcytosine).

The methylation status can optionally be represented or indicated by a“methylation value” (e.g., representing a methylation frequency,fraction, ratio, percent, etc.) A methylation value can be generated,for example, by quantifying the amount of intact nucleic acid presentfollowing restriction digestion with a methylation dependent restrictionenzyme or by comparing amplification profiles after bisulfite reactionor by comparing sequences of bisulfite-treated and untreated nucleicacids. Accordingly, a value, e.g., a methylation value, represents themethylation status and can thus be used as a quantitative indicator ofmethylation status across multiple copies of a locus. This is ofparticular use when it is desirable to compare the methylation status ofa sequence in a sample to a threshold or reference value.

As used herein, “methylation frequency” or “methylation percent (%)”refer to the number of instances in which a molecule or locus ismethylated relative to the number of instances the molecule or locus isunmethylated.

As such, the methylation state describes the state of methylation of anucleic acid (e.g., a genomic sequence). In addition, the methylationstate refers to the characteristics of a nucleic acid segment at aparticular genomic locus relevant to methylation. Such characteristicsinclude, but are not limited to, whether any of the cytosine (C)residues within this DNA sequence are methylated, the location ofmethylated C residue(s), the frequency or percentage of methylated Cthroughout any particular region of a nucleic acid, and allelicdifferences in methylation due to, e.g., difference in the origin of thealleles. The terms “methylation state”, “methylation profile”, and“methylation status” also refer to the relative concentration, absoluteconcentration, or pattern of methylated C or unmethylated C throughoutany particular region of a nucleic acid in a biological sample. Forexample, if the cytosine (C) residue(s) within a nucleic acid sequenceare methylated it may be referred to as “hypermethylated” or having“increased methylation”, whereas if the cytosine (C) residue(s) within aDNA sequence are not methylated it may be referred to as“hypomethylated” or having “decreased methylation”. Likewise, if thecytosine (C) residue(s) within a nucleic acid sequence are methylated ascompared to another nucleic acid sequence (e.g., from a different regionor from a different individual, etc.) that sequence is consideredhypermethylated or having increased methylation compared to the othernucleic acid sequence. Alternatively, if the cytosine (C) residue(s)within a DNA sequence are not methylated as compared to another nucleicacid sequence (e.g., from a different region or from a differentindividual, etc.) that sequence is considered hypomethylated or havingdecreased methylation compared to the other nucleic acid sequence.Additionally, the term “methylation pattern” as used herein refers tothe collective sites of methylated and unmethylated nucleotides over aregion of a nucleic acid. Two nucleic acids may have the same or similarmethylation frequency or methylation percent but have differentmethylation patterns when the number of methylated and unmethylatednucleotides are the same or similar throughout the region but thelocations of methylated and unmethylated nucleotides are different.Sequences are said to be “differentially methylated” or as having a“difference in methylation” or having a “different methylation state”when they differ in the extent (e.g., one has increased or decreasedmethylation relative to the other), frequency, or pattern ofmethylation. The term “differential methylation” refers to a differencein the level or pattern of nucleic acid methylation in a cancer positivesample as compared with the level or pattern of nucleic acid methylationin a cancer negative sample. It may also refer to the difference inlevels or patterns between patients that have recurrence of cancer aftersurgery versus patients who not have recurrence. Differentialmethylation and specific levels or patterns of DNA methylation areprognostic and predictive biomarkers, e.g., once the correct cut-off orpredictive characteristics have been defined.

Methylation state frequency can be used to describe a population ofindividuals or a sample from a single individual. For example, anucleotide locus having a methylation state frequency of 50% ismethylated in 50% of instances and unmethylated in 50% of instances.Such a frequency can be used, for example, to describe the degree towhich a nucleotide locus or nucleic acid region is methylated in apopulation of individuals or a collection of nucleic acids. Thus, whenmethylation in a first population or pool of nucleic acid molecules isdifferent from methylation in a second population or pool of nucleicacid molecules, the methylation state frequency of the first populationor pool will be different from the methylation state frequency of thesecond population or pool. Such a frequency also can be used, forexample, to describe the degree to which a nucleotide locus or nucleicacid region is methylated in a single individual. For example, such afrequency can be used to describe the degree to which a group of cellsfrom a tissue sample are methylated or unmethylated at a nucleotidelocus or nucleic acid region.

The term “highly methylated” refers to nucleic acids in which aparticular locus (e.g., a CpG dinucleotide or set of dinucleotides orCpG-rich region) is methylated in a particular sample type or tissuetype at a rate that is measurably greater than is observed for thecomparable locus in the same DNA in another tissue or sample type.“Highly methylated” may refer to a single particular C-residue or to anaverage rate of methylation across multiple Cs in a region, as afraction of the copies of that locus in the sample being assayed.Without limiting the term to any particular level of methylation, insome embodiments, a highly methylated locus may be >10% methylated,preferably >20% to 40%, more preferably >50% to 75%, still morepreferably between 75% and 100%.

As used herein a “nucleotide locus” refers to the location of anucleotide in a nucleic acid molecule. A nucleotide locus of amethylated nucleotide refers to the location of a methylated nucleotidein a nucleic acid molecule.

Typically, methylation of human DNA occurs on a dinucleotide sequenceincluding an adjacent guanine and cytosine where the cytosine is located5′ of the guanine (also termed CpG dinucleotide sequences). Mostcytosines within the CpG dinucleotides are methylated in the humangenome, however some remain unmethylated in specific CpG dinucleotiderich genomic regions, known as CpG islands (see, e.g., Antequera et al.(1990) Cell 62: 503-514).

As used herein, a “CpG island” refers to a G:C-rich region of genomicDNA containing an increased number of CpG dinucleotides relative tototal genomic DNA. A CpG island can be at least 100, 200, or more basepairs in length, where the G:C content of the region is at least 50% andthe ratio of observed CpG frequency over expected frequency is 0.6; insome instances, a CpG island can be at least 500 base pairs in length,where the G:C content of the region is at least 55%) and the ratio ofobserved CpG frequency over expected frequency is 0.65. The observed CpGfrequency over expected frequency can be calculated according to themethod provided in Gardiner-Garden et al (1987) J. Mol. Biol. 196:261-281. For example, the observed CpG frequency over expected frequencycan be calculated according to the formula R=(A×B)/(C×D), where R is theratio of observed CpG frequency over expected frequency, A is the numberof CpG dinucleotides in an analyzed sequence, B is the total number ofnucleotides in the analyzed sequence, C is the total number of Cnucleotides in the analyzed sequence, and D is the total number of Gnucleotides in the analyzed sequence. Methylation state is typicallydetermined in CpG islands, e.g., at promoter regions. It will beappreciated though that other sequences in the human genome are prone toDNA methylation such as CpA and CpT (see Ramsahoye (2000) Proc. Natl.Acad. Sci. USA 97: 5237-5242; Salmon and Kaye (1970) Biochim. Biophys.Acta. 204: 340-351; Grafstrom (1985) Nucleic Acids Res. 13: 2827-2842;Nyce (1986) Nucleic Acids Res. 14: 4353-4367; Woodcock (1987) Biochem.Biophys. Res. Commun. 145: 888-894).

As used herein, the term “tissue cell” refers to any tissue cell in abody, e.g., a human or animal body, including, e.g., epithelium, muscle,nerve, and bone cells. Tissue cells do not include blood cells. As usedherein, blood normally comprises plasma, red blood cells, white bloodcells (including leukocytes and lymphocytes), and platelets. Leukocytesinclude neutophils, monocytes, eosinophils and basophils, andlymphocytes include T cells, B cells and natural killer cells.

“Tissue cell-specific control DNA” and “tissue cell-specific DNA referto DNA that is detectable of the presence of tissue or in cell-free DNAfrom tissue, and that is minimally detectable or undetectable in bloodor in a normal component of blood (e.g., plasma, white blood cells,etc., as listed above). As used herein, DNA that is methylated only intissue and is not similarly methylated in blood (or vice versa) may betissue-cell specific DNA with respect to the methylation state, even ifthe primary sequence of the DNA is the same in both cell types.“Epithelium-specific control DNA” refers to tissue-specific control DNAthat detects DNA found in epithelial cells.

As used herein, a reagent that modifies a nucleotide of the nucleic acidmolecule as a function of the methylation state of the nucleic acidmolecule, or a methylation-specific reagent, refers to a compound orcomposition or other agent that can change the nucleotide sequence of anucleic acid molecule in a manner that reflects the methylation state ofthe nucleic acid molecule. Methods of treating a nucleic acid moleculewith such a reagent can include contacting the nucleic acid moleculewith the reagent, coupled with additional steps, if desired, toaccomplish the desired change of nucleotide sequence. Such a change inthe nucleic acid molecule's nucleotide sequence can result in a nucleicacid molecule in which each methylated nucleotide is modified to adifferent nucleotide. Such a change in the nucleic acid nucleotidesequence can result in a nucleic acid molecule in which eachunmethylated nucleotide is modified to a different nucleotide. Such achange in the nucleic acid nucleotide sequence can result in a nucleicacid molecule in which each of a selected nucleotide which isunmethylated (e.g., each unmethylated cytosine) is modified to adifferent nucleotide. Use of such a reagent to change the nucleic acidnucleotide sequence can result in a nucleic acid molecule in which eachnucleotide that is a methylated nucleotide (e.g., each methylatedcytosine) is modified to a different nucleotide. As used herein, use ofa reagent that modifies a selected nucleotide refers to a reagent thatmodifies one nucleotide of the four typically occurring nucleotides in anucleic acid molecule (C, G, T, and A for DNA and C, G, U, and A forRNA), such that the reagent modifies the one nucleotide withoutmodifying the other three nucleotides. In one exemplary embodiment, sucha reagent modifies an unmethylated selected nucleotide to produce adifferent nucleotide. In another exemplary embodiment, such a reagentcan deaminate unmethylated cytosine nucleotides. An exemplary reagent isbisulfite.

As used herein, the term “bisulfite reagent” refers to a reagentcomprising in some embodiments bisulfite, disulfite, hydrogen sulfite,or combinations thereof to distinguish between methylated andunmethylated cytidines, e.g., in CpG dinucleotide sequences. The term“methylation assay” refers to any assay for determining the methylationstate of one or more CpG dinucleotide sequences within a sequence of anucleic acid.

The term “MS AP-PCR” (Methylation-Sensitive Arbitrarily-PrimedPolymerase Chain Reaction) refers to the art-recognized technology thatallows for a global scan of the genome using CG-rich primers to focus onthe regions most likely to contain CpG dinucleotides, and described byGonzalgo et al. (1997) Cancer Research 57: 594-599.

The term “MethyLight™” refers to the art-recognized fluorescence-basedreal-time PCR technique described by Eads et al. (1999) Cancer Res. 59:2302-2306.

The term “HeavyMethyl™” refers to an assay wherein methylation specificblocking probes (also referred to herein as blockers) covering CpGpositions between, or covered by, the amplification primers enablemethylation-specific selective amplification of a nucleic acid sample.

The term “HeavyMethyl™ MethyLight™” assay refers to a HeavyMethyl™MethyLight™ assay, which is a variation of the MethyLight™ assay,wherein the MethyLight™ assay is combined with methylation specificblocking probes covering CpG positions between the amplificationprimers.

The term “Ms-SNuPE” (Methylation-sensitive Single Nucleotide PrimerExtension) refers to the art-recognized assay described by Gonzalgo &Jones (1997) Nucleic Acids Res. 25: 2529-2531.

The term “MSP” (Methylation-specific PCR) refers to the art-recognizedmethylation assay described by Herman et al. (1996) Proc. Natl. Acad.Sci. USA 93: 9821-9826, and by U.S. Pat. No. 5,786,146.

The term “COBRA” (Combined Bisulfite Restriction Analysis) refers to theart-recognized methylation assay described by Xiong & Laird (1997)Nucleic Acids Res. 25: 2532-2534.

The term “MCA” (Methylated CpG Island Amplification) refers to themethylation assay described by Toyota et al. (1999) Cancer Res. 59:2307-12, and in WO 00/26401A1.

As used herein, the term “kit” refers to any delivery system fordelivering materials. In the context of nucleic acid purificationsystems and reaction assays, such delivery systems include systems thatallow for the storage, transport, or delivery of reagents and devices(e.g., inhibitor adsorbants, particles, denaturants, oligonucleotides,spin filters etc. in the appropriate containers) and/or supportingmaterials (e.g., buffers, written instructions for performing aprocedure, etc.) from one location to another. For example, kits includeone or more enclosures (e.g., boxes) containing the relevant reactionreagents and/or supporting materials. As used herein, the term“fragmented kit” refers to a delivery system comprising two or moreseparate containers that each contains a subportion of the total kitcomponents. The containers may be delivered to the intended recipienttogether or separately. For example, a first container may containmaterials for sample collection and a buffer, while a second containercontains capture oligonucleotides and denaturant. The term “fragmentedkit” is intended to encompass kits containing Analyte specific reagents(ASR's) regulated under section 520(e) of the Federal Food, Drug, andCosmetic Act, but are not limited thereto. Indeed, any delivery systemcomprising two or more separate containers that each contains asubportion of the total kit components are included in the term“fragmented kit.” In contrast, a “combined kit” refers to a deliverysystem containing all of the components of a reaction assay in a singlecontainer (e.g., in a single box housing each of the desiredcomponents). The term “kit” includes both fragmented and combined kits.

The term “system” as used herein refers to a collection of articles foruse for a particular purpose. In some embodiments, the articles compriseinstructions for use, as information supplied on e.g., an article, onpaper, or on recordable media (e.g., diskette, CD, flash drive, etc.).In some embodiments, instructions direct a user to an online location,e.g., a website.

As used herein, the term “information” refers to any collection of factsor data. In reference to information stored or processed using acomputer system(s), including but not limited to internets, the termrefers to any data stored in any format (e.g., analog, digital, optical,etc.). As used herein, the term “information related to a subject”refers to facts or data pertaining to a subject (e.g., a human, plant,or animal). The term “genomic information” refers to informationpertaining to a genome including, but not limited to, nucleic acidsequences, genes, percentage methylation, allele frequencies, RNAexpression levels, protein expression, phenotypes correlating togenotypes, etc. “Allele frequency information” refers to facts or datapertaining to allele frequencies, including, but not limited to, alleleidentities, statistical correlations between the presence of an alleleand a characteristic of a subject (e.g., a human subject), the presenceor absence of an allele in an individual or population, the percentagelikelihood of an allele being present in an individual having one ormore particular characteristics, etc.

DETAILED DESCRIPTION

Provided herein is technology relating to performing assays fordetection and quantification of DNA, e.g., methylated DNA. Inparticular, the technology relates to internal controls for suchmethylation assays.

Embodiments of the present disclosure provide a marker termed “ZDHHC1”for use as a methylation marker and internal control. Experimentsconducted during the development of embodiments of the disclosuredemonstrated that little or no methylated ZDHHC1 is found in normalblood samples (e.g., obtained from disease-free individuals). Incontrast to commonly used internal control DNAs (e.g., β-actin), ZDHHC1gives a very low background signal, e.g., from blood present in a tissueor stool sample. During development of the present technology, it wasfound that replacing the ACTB internal control with ZDHHC1 in anexemplary methylation assay (e.g. a flap endonuclease assay, such as aQUARTS assay) increased the sensitivity and specificity of the assay.

Further experiments demonstrated that ZDHHC1 serves as a marker thatfinds use in detecting epithelial tissue cells in blood (e.g., as amarker for metastatic cancer). Exemplary embodiments are describedherein.

Although the disclosure herein refers to certain illustratedembodiments, it is to be understood that these embodiments are presentedby way of example and not by way of limitation.

I. Tissue Cell—Specific Markers

In assays that detect and quantify methylated CpG-rich DNA that hasundergone bisulfite conversion, it is typical to also detect a controlgene present in the same sample, the control gene verifying the DNAinput in the assay regardless of source (e.g., cancer, normal, stool,tissue). Such a control gene is used, for example, to normalize DNA copynumber data obtained in assays across different samples, to accuratelyshow higher or lower disease-associated marker levels sample-to-sample.

For a methylation assay normalizing gene to work best, it should meetseveral criteria. An ideal normalizing gene, for example: 1) should beequally present in both normal and diseased tissue; 2) should haveapproximately the same GC content as the test gene(s)/marker(s) that arebeing assayed (e.g., DNA markers in which hypermethylation is anindicator of a disease state); 3) should react in the same manner as thetest genes/markers to pre-quantification (pre-PCR) sample treatments,such as bisulfite conversion; and 4) should have PCR amplificationefficiency that is similar to that of the test genes/markers beingassayed.

The β-actin gene, a gene typically used as a normalizing gene fordetection of methylated marker DNAs, does not have the same GC contentand CpG methylation as methylation markers associated with diseases suchas cancer and adenoma (e.g., vimentin, septin 9, NDRG4, BMP3), so itdoes not behave like such marker DNAs in pre-PCR bisulfite conversion orin PCR amplification. In the development of the instant technology, ithas been found that use of a normalizing gene that meets the criteriadiscussed above in place of ACTB improves assay sensitivity andspecificity. In the development of the instant technology, it hasfurther been found that use of a marker gene that is highly methylatedin both normal and diseased tissue, but that is not methylated in bloodprovides a marker that is specific for tissue cells, e.g., epithelialcells, and that has a low presence in blood. Use of such control DNAsreduces background from any blood present in sample (e.g., a stool ortissue sample), and it also can be used to detect an abnormal presenceof such tissue cells in blood, as may occur, e.g., during metastasisfrom a tumor.

Experiments described herein identified genes (e.g., ZDHHC1) that arehighly methylated in normal and cancer tissue. These genes are nothighly methylated in blood, and the degree to which they are methylatedin blood does not change in accordance with a disease state, except asdescribed in Example 6, in association with metastatic cancer. Thisallows for better and more accurate methylation calculation that isreflective of tissue only, and is independent of blood content in asample. The genes described herein are used to normalize marker levelsacross patients and samples.

ZDHHC1, ZFAND3, ZMYM4, ODZ2, and TRIO were identified as candidatemethylation markers. The selection of normalizing genes having lowmethylation in buffy coat allows for more sensitive detection ofmethylation of markers of interest (e.g., the denominator used fornormalizing signal is low, and therefore, % methylation of the marker ofinterest becomes larger and easier to distinguish).

The normalizing genes described herein are highly methylated in tissue(cancer and normal) and are not highly methylated in blood, and provideseveral advantages over existing markers:

-   -   1—GC-content and CpG methylation and bisulfate reactivity are        more similar to the DNA marker(s) being studied.    -   2—They display PCR amplification efficiency that is more similar        to that of the marker DNA being measured.    -   3—Low methylation state in buffy coat allows higher percent        methylation detection of markers of interest in blood or in the        presence of blood.

II. Methylation Detection Assays

The markers described herein (e.g., ZDHHC1 in particular), find use in avariety of methylation detection assays as normalization reagents andindicators of disease states.

The most frequently used method for analyzing a nucleic acid for thepresence of 5-methylcytosine is based upon the bisulfite methoddescribed by Frommer, et al. for the detection of 5-methylcytosines inDNA (Frommer et al. (1992) Proc. Natl. Acad. Sci. USA 89: 1827-31explicitly incorporated herein by reference in its entirety for allpurposes) or variations thereof. The bisulfite method of mapping5-methylcytosines is based on the observation that cytosine, but not5-methylcytosine, reacts with hydrogen sulfite ion (also known asbisulfite). The reaction is usually performed according to the followingsteps: first, cytosine reacts with hydrogen sulfite to form a sulfonatedcytosine. Next, spontaneous deamination of the sulfonated reactionintermediate results in a sulfonated uracil. Finally, the sulfonateduracil is desulfonated under alkaline conditions to form uracil.Detection is possible because uracil base pairs with adenine (thusbehaving like thymine), whereas 5-methylcytosine base pairs with guanine(thus behaving like cytosine). This makes the discrimination ofmethylated cytosines from non-methylated cytosines possible by, e.g.,bisulfite genomic sequencing (Grigg G, & Clark S, Bioessays (1994) 16:431-36; Grigg G, DNA Seq. (1996) 6: 189-98), methylation-specific PCR(MSP) as is disclosed, e.g., in U.S. Pat. No. 5,786,146, or using anassay comprising sequence-specific probe cleavage, e.g., a QuARTS flapendonuclease assay (see, e.g., Zou et al. (2010) “Sensitivequantification of methylated markers with a novel methylation specifictechnology” Clin Chem 56: A199; U.S. Pat. No. 8,361,720, and U.S. patentapplication Ser. Nos. 12/946,745; 12/946,752, and 61/705,603).

Some conventional technologies are related to methods comprisingenclosing the DNA to be analyzed in an agarose matrix, therebypreventing the diffusion and renaturation of the DNA (bisulfite onlyreacts with single-stranded DNA), and replacing precipitation andpurification steps with a fast dialysis (Olek A, et al. (1996) “Amodified and improved method for bisulfite based cytosine methylationanalysis” Nucleic Acids Res. 24: 5064-6). It is thus possible to analyzeindividual cells for methylation status, illustrating the utility andsensitivity of the method. An overview of conventional methods fordetecting 5-methylcytosine is provided by Rein, T., et al. (1998)Nucleic Acids Res. 26: 2255.

The bisulfite technique typically involves amplifying short, specificfragments of a known nucleic acid subsequent to a bisulfite treatment,then either assaying the product by sequencing (Olek & Walter (1997)Nat. Genet. 17: 275-6) or a primer extension reaction (Gonzalgo & Jones(1997) Nucleic Acids Res. 25: 2529-31; WO 95/00669; U.S. Pat. No.6,251,594) to analyze individual cytosine positions. Some methods useenzymatic digestion (Xiong & Laird (1997) Nucleic Acids Res. 25:2532-4). Detection by hybridization has also been described in the art(Olek et al., WO 99/28498). Additionally, use of the bisulfite techniquefor methylation detection with respect to individual genes has beendescribed (Grigg & Clark (1994) Bioessays 16: 431-6; Zeschnigk et al.(1997) Hum Mol Genet. 6: 387-95; Feil et al. (1994) Nucleic Acids Res.22: 695; Martin et al. (1995) Gene 157: 261-4; WO 9746705; WO 9515373).

Various methylation assay procedures can be used in conjunction withbisulfite treatment according to the present technology. These assaysallow for determination of the methylation state of one or a pluralityof CpG dinucleotides (e.g., CpG islands) within a nucleic acid sequence.Such assays involve, among other techniques, sequencing ofbisulfite-treated nucleic acid, PCR (for sequence-specificamplification), Southern blot analysis, and use of methylation-sensitiverestriction enzymes.

For example, genomic sequencing has been simplified for analysis ofmethylation patterns and 5-methylcytosine distributions by usingbisulfite treatment (Frommer et al. (1992) Proc. Natl. Acad. Sci. USA89: 1827-1831). Additionally, restriction enzyme digestion of PCRproducts amplified from bisulfite-converted DNA finds use in assessingmethylation state, e.g., as described by Sadri & Hornsby (1997) Nucl.Acids Res. 24: 5058-5059 or as embodied in the method known as COBRA(Combined Bisulfite Restriction Analysis) (Xiong & Laird (1997) NucleicAcids Res. 25: 2532-2534).

COBRA™ analysis is a quantitative methylation assay useful fordetermining DNA methylation levels at specific loci in small amounts ofgenomic DNA (Xiong & Laird, Nucleic Acids Res. 25:2532-2534, 1997).Briefly, restriction enzyme digestion is used to revealmethylation-dependent sequence differences in PCR products of sodiumbisulfite-treated DNA. Methylation-dependent sequence differences arefirst introduced into the genomic DNA by standard bisulfite treatmentaccording to the procedure described by Frommer et al. (Proc. Natl.Acad. Sci. USA 89:1827-1831, 1992). PCR amplification of the bisulfiteconverted DNA is then performed using primers specific for the CpGislands of interest, followed by restriction endonuclease digestion, gelelectrophoresis, and detection using specific, labeled hybridizationprobes. Methylation levels in the original DNA sample are represented bythe relative amounts of digested and undigested PCR product in alinearly quantitative fashion across a wide spectrum of DNA methylationlevels. In addition, this technique can be reliably applied to DNAobtained from microdissected paraffin-embedded tissue samples.

Typical reagents (e.g., as might be found in a typical COBRA™-based kit)for COBRA™ analysis may include, but are not limited to: PCR primers forspecific loci (e.g., specific genes, markers, regions of genes, regionsof markers, bisulfite treated DNA sequence, CpG island, etc.);restriction enzyme and appropriate buffer; gene-hybridizationoligonucleotide; control hybridization oligonucleotide; kinase labelingkit for oligonucleotide probe; and labeled nucleotides. Additionally,bisulfite conversion reagents may include: DNA denaturation buffer;sulfonation buffer; DNA recovery reagents or kits (e.g., precipitation,ultrafiltration, affinity column); desulfonation buffer; and DNArecovery components.

Assays such as “MethyLight™” (a fluorescence-based real-time PCRtechnique) (Eads et al., Cancer Res. 59:2302-2306, 1999), Ms-SNuPE™(Methylation-sensitive Single Nucleotide Primer Extension) reactions(Gonzalgo & Jones, Nucleic Acids Res. 25:2529-2531, 1997),methylation-specific PCR (“MSP”; Herman et al., Proc. Natl. Acad. Sci.USA 93:9821-9826, 1996; U.S. Pat. No. 5,786,146), and methylated CpGisland amplification (“MCA”; Toyota et al., Cancer Res. 59:2307-12,1999) are used alone or in combination with one or more of thesemethods.

The “HeavyMethyl™” assay, technique is a quantitative method forassessing methylation differences based on methylation-specificamplification of bisulfite-treated DNA. Methylation-specific blockingprobes (“blockers”) covering CpG positions between, or covered by, theamplification primers enable methylation-specific selectiveamplification of a nucleic acid sample.

The term “HeavyMethyl™ MethyLight™” assay refers to a HeavyMethyl™MethyLight™ assay, which is a variation of the MethyLight™ assay,wherein the MethyLight™ assay is combined with methylation specificblocking probes covering CpG positions between the amplificationprimers. The HeavyMethyl™ assay may also be used in combination withmethylation specific amplification primers.

Typical reagents (e.g., as might be found in a typical MethyLight™-basedkit) for HeavyMethyl™ analysis may include, but are not limited to: PCRprimers for specific loci (e.g., specific genes, markers, regions ofgenes, regions of markers, bisulfite treated DNA sequence, CpG island,or bisulfite treated DNA sequence or CpG island, etc.); blockingoligonucleotides; optimized PCR buffers and deoxynucleotides; and Taqpolymerase.

MSP (methylation-specific PCR) allows for assessing the methylationstatus of virtually any group of CpG sites within a CpG island,independent of the use of methylation-sensitive restriction enzymes(Herman et al. Proc. Natl. Acad. Sci. USA 93:9821-9826, 1996; U.S. Pat.No. 5,786,146). Briefly, DNA is modified by sodium bisulfite, whichconverts unmethylated, but not methylated cytosines, to uracil, and theproducts are subsequently amplified with primers specific for methylatedversus unmethylated DNA. MSP requires only small quantities of DNA, issensitive to 0.1% methylated alleles of a given CpG island locus, andcan be performed on DNA extracted from paraffin-embedded samples.Typical reagents (e.g., as might be found in a typical MSP-based kit)for MSP analysis may include, but are not limited to: methylated andunmethylated PCR primers for specific loci (e.g., specific genes,markers, regions of genes, regions of markers, bisulfite treated DNAsequence, CpG island, etc.); optimized PCR buffers and deoxynucleotides,and specific probes.

The MethyLight™ assay is a high-throughput quantitative methylationassay that utilizes fluorescence-based real-time PCR (e.g., TaqMan®)that requires no further manipulations after the PCR step (Eads et al.,Cancer Res. 59:2302-2306, 1999). Briefly, the MethyLight™ process beginswith a mixed sample of genomic DNA that is converted, in a sodiumbisulfite reaction, to a mixed pool of methylation-dependent sequencedifferences according to standard procedures (the bisulfite processconverts unmethylated cytosine residues to uracil). Fluorescence-basedPCR is then performed in a “biased” reaction, e.g., with PCR primersthat overlap known CpG dinucleotides. Sequence discrimination occursboth at the level of the amplification process and at the level of thefluorescence detection process.

The MethyLight™ assay is used as a quantitative test for methylationpatterns in a nucleic acid, e.g., a genomic DNA sample, wherein sequencediscrimination occurs at the level of probe hybridization. In aquantitative version, the PCR reaction provides for a methylationspecific amplification in the presence of a fluorescent probe thatoverlaps a particular putative methylation site. An unbiased control forthe amount of input DNA is provided by a reaction in which neither theprimers, nor the probe, overlie any CpG dinucleotides. Alternatively, aqualitative test for genomic methylation is achieved by probing thebiased PCR pool with either control oligonucleotides that do not coverknown methylation sites (e.g., a fluorescence-based version of theHeavyMethyl™ and MSP techniques) or with oligonucleotides coveringpotential methylation sites.

The MethyLight™ process is used with any suitable probe (e.g. a“TaqMan®” probe, a Lightcycler® probe, etc.) For example, in someapplications double-stranded genomic DNA is treated with sodiumbisulfite and subjected to one of two sets of PCR reactions usingTaqMan® probes, e.g., with MSP primers and/or HeavyMethyl blockeroligonucleotides and a TaqMan® probe. The TaqMan® probe is dual-labeledwith fluorescent “reporter” and “quencher” molecules and is designed tobe specific for a relatively high GC content region so that it melts atabout a 10° C. higher temperature in the PCR cycle than the forward orreverse primers. This allows the TaqMan® probe to remain fullyhybridized during the PCR annealing/extension step. As the Taqpolymerase enzymatically synthesizes a new strand during PCR, it willeventually reach the annealed TaqMan® probe. The Taq polymerase 5′ to 3′endonuclease activity will then displace the TaqMan® probe by digestingit to release the fluorescent reporter molecule for quantitativedetection of its now unquenched signal using a real-time fluorescentdetection system.

Typical reagents (e.g., as might be found in a typical MethyLight™-basedkit) for MethyLight™ analysis may include, but are not limited to: PCRprimers for specific loci (e.g., specific genes, markers, regions ofgenes, regions of markers, bisulfite treated DNA sequence, CpG island,etc.); TaqMan® or Lightcycler® probes; optimized PCR buffers anddeoxynucleotides; and Taq polymerase.

The QM™ (quantitative methylation) assay is an alternative quantitativetest for methylation patterns in genomic DNA samples, wherein sequencediscrimination occurs at the level of probe hybridization. In thisquantitative version, the PCR reaction provides for unbiasedamplification in the presence of a fluorescent probe that overlaps aparticular putative methylation site. An unbiased control for the amountof input DNA is provided by a reaction in which neither the primers, northe probe, overlie any CpG dinucleotides. Alternatively, a qualitativetest for genomic methylation is achieved by probing the biased PCR poolwith either control oligonucleotides that do not cover known methylationsites (a fluorescence-based version of the HeavyMethyl™ and MSPtechniques) or with oligonucleotides covering potential methylationsites.

The QM™ process can be used with any suitable probe, e.g., “TaqMan®”probes, Lightcycler® probes, in the amplification process. For example,double-stranded genomic DNA is treated with sodium bisulfite andsubjected to unbiased primers and the TaqMan® probe. The TaqMan® probeis dual-labeled with fluorescent “reporter” and “quencher” molecules,and is designed to be specific for a relatively high GC content regionso that it melts out at about a 10° C. higher temperature in the PCRcycle than the forward or reverse primers. This allows the TaqMan® probeto remain fully hybridized during the PCR annealing/extension step. Asthe Taq polymerase enzymatically synthesizes a new strand during PCR, itwill eventually reach the annealed TaqMan® probe. The Taq polymerase 5′to 3′ endonuclease activity will then displace the TaqMan® probe bydigesting it to release the fluorescent reporter molecule forquantitative detection of its now unquenched signal using a real-timefluorescent detection system. Typical reagents (e.g., as might be foundin a typical QM™-based kit) for QM™ analysis may include, but are notlimited to: PCR primers for specific loci (e.g., specific genes,markers, regions of genes, regions of markers, bisulfite treated DNAsequence, CpG island, etc.); TaqMan® or Lightcycler® probes; optimizedPCR buffers and deoxynucleotides; and Taq polymerase. The Ms-SNuPE™technique is a quantitative method for assessing methylation differencesat specific CpG sites based on bisulfite treatment of DNA, followed bysingle-nucleotide primer extension (Gonzalgo & Jones, Nucleic Acids Res.25:2529-2531, 1997). Briefly, genomic DNA is reacted with sodiumbisulfite to convert unmethylated cytosine to uracil while leaving5-methylcytosine unchanged. Amplification of the desired target sequenceis then performed using PCR primers specific for bisulfite-convertedDNA, and the resulting product is isolated and used as a template formethylation analysis at the CpG site of interest. Small amounts of DNAcan be analyzed (e.g., microdissected pathology sections) and it avoidsutilization of restriction enzymes for determining the methylationstatus at CpG sites.

Typical reagents (e.g., as might be found in a typical Ms-SNuPE™-basedkit) for Ms-SNuPE™ analysis may include, but are not limited to: PCRprimers for specific loci (e.g., specific genes, markers, regions ofgenes, regions of markers, bisulfite treated DNA sequence, CpG island,etc.); optimized PCR buffers and deoxynucleotides; gel extraction kit;positive control primers; Ms-SNuPE™ primers for specific loci; reactionbuffer (for the Ms-SNuPE reaction); and labeled nucleotides.Additionally, bisulfite conversion reagents may include: DNAdenaturation buffer; sulfonation buffer; DNA recovery reagents or kit(e.g., precipitation, ultrafiltration, affinity column); desulfonationbuffer; and DNA recovery components. Reduced Representation BisulfiteSequencing (RRBS) begins with bisulfite treatment of nucleic acid toconvert all unmethylated cytosines to uracil, followed by restrictionenzyme digestion (e.g., by an enzyme that recognizes a site including aCG sequence such as MspI) and complete sequencing of fragments aftercoupling to an adapter ligand. The choice of restriction enzyme enrichesthe fragments for CpG dense regions, reducing the number of redundantsequences that may map to multiple gene positions during analysis. Assuch, RRBS reduces the complexity of the nucleic acid sample byselecting a subset (e.g., by size selection using preparative gelelectrophoresis) of restriction fragments for sequencing. As opposed towhole-genome bisulfite sequencing, every fragment produced by therestriction enzyme digestion contains DNA methylation information for atleast one CpG dinucleotide. As such, RRBS enriches the sample forpromoters, CpG islands, and other genomic features with a high frequencyof restriction enzyme cut sites in these regions and thus provides anassay to assess the methylation state of one or more genomic loci.

A typical protocol for RRBS comprises the steps of digesting a nucleicacid sample with a restriction enzyme such as MspI, filling in overhangsand A-tailing, ligating adaptors, bisulfite conversion, and PCR. See,e.g., et al. (2005) “Genome-scale DNA methylation mapping of clinicalsamples at single-nucleotide resolution” Nat Methods 7: 133-6; Meissneret al. (2005) “Reduced representation bisulfite sequencing forcomparative high-resolution DNA methylation analysis” Nucleic Acids Res.33: 5868-77.

In some embodiments, a quantitative allele-specific real-time target andsignal amplification (QuARTS) assay is used to evaluate methylationstate. Three reactions sequentially occur in each QuARTS assay,including amplification (reaction 1) and target probe cleavage (reaction2) in the primary reaction; and FRET cleavage and fluorescent signalgeneration (reaction 3) in the secondary reaction. When target nucleicacid is amplified with specific primers, a specific detection probe witha flap sequence loosely binds to the amplicon. The presence of thespecific invasive oligonucleotide at the target binding site causes a 5′nuclease, e.g., a FEN-1 endonuclease, to release the flap sequence bycutting between the detection probe and the flap sequence. The flapsequence is complementary to a non-hairpin portion of a correspondingFRET cassette. Accordingly, the flap sequence functions as an invasiveoligonucleotide on the FRET cassette and effects a cleavage between theFRET cassette fluorophore and a quencher, which produces a fluorescentsignal. The cleavage reaction can cut multiple probes per target andthus release multiple fluorophore per flap, providing exponential signalamplification. QuARTS can detect multiple targets in a single reactionwell by using FRET cassettes with different dyes. See, e.g., in Zou etal. (2010) “Sensitive quantification of methylated markers with a novelmethylation specific technology” Clin Chem 56: A199).

The term “bisulfite reagent” refers to a reagent comprising bisulfite,disulfite, hydrogen sulfite, or combinations thereof, useful asdisclosed herein to distinguish between methylated and unmethylated CpGdinucleotide sequences. Methods of said treatment are known in the art(e.g., PCT/EP2004/011715 and WO 2013/116375, each of which isincorporated by reference in its entirety). In some embodiments,bisulfite treatment is conducted in the presence of denaturing solventssuch as but not limited to n-alkylenglycol or diethylene glycol dimethylether (DME), or in the presence of dioxane or dioxane derivatives. Insome embodiments the denaturing solvents are used in concentrationsbetween 1% and 35% (v/v). In some embodiments, the bisulfite reaction iscarried out in the presence of scavengers such as but not limited tochromane derivatives, e.g., 6-hydroxy-2,5,7,8,-tetramethylchromane2-carboxylic acid or trihydroxybenzone acid and derivates thereof, e.g.,Gallic acid (see: PCT/EP2004/011715, which is incorporated by referencein its entirety). In certain preferred embodiments, the bisulfitereaction comprises treatment with ammonium hydrogen sulfite, e.g., asdescribed in WO 2013/116375.

In some embodiments, the bisulfite-treated DNA is purified prior to thequantification. This may be conducted by any means known in the art,such as but not limited to ultrafiltration, e.g., by means of Microcon™columns (manufactured by Millipore™). The purification is carried outaccording to a modified manufacturer's protocol (see, e.g.,PCT/EP2004/011715, which is incorporated by reference in its entirety).In some embodiments, the bisulfite treated DNA is bound to a solidsupport, e.g., a magnetic bead, and desulfonation and washing occurswhile the DNA is bound to the support. Examples of such embodiments areprovided, e.g., in WO 2013/116375. In certain preferred embodiments,support-bound DNA is ready for a methylation assay immediately afterdesulfonation and washing on the support. In some embodiments, thedesulfonated DNA is eluted from the support prior to assay.

In some embodiments, fragments of the treated DNA are amplified usingsets of primer oligonucleotides according to the present invention(e.g., see Table 2) and an amplification enzyme. The amplification ofseveral DNA segments can be carried out simultaneously in one and thesame reaction vessel. Typically, the amplification is carried out usinga polymerase chain reaction (PCR).

In another embodiment of the method, the methylation status of CpGpositions within or near a marker are detected by use ofmethylation-specific primer oligonucleotides. This technique (MSP) hasbeen described in U.S. Pat. No. 6,265,171 to Herman. The use ofmethylation status specific primers for the amplification of bisulfitetreated DNA allows the differentiation between methylated andunmethylated nucleic acids. MSP primer pairs contain at least one primerthat hybridizes to a bisulfite treated CpG dinucleotide. Therefore, thesequence of said primers comprises at least one CpG dinucleotide. MSPprimers specific for non-methylated DNA contain a “T” at the position ofthe C position in the CpG. The fragments obtained by means of theamplification can carry a directly or indirectly detectable label. Insome embodiments, the labels are fluorescent labels, radionuclides, ordetachable molecule fragments having a typical mass that can be detectedin a mass spectrometer. Where said labels are mass labels, someembodiments provide that the labeled amplicons have a single positive ornegative net charge, allowing for better delectability in the massspectrometer. The detection may be carried out and visualized by meansof, e.g., matrix assisted laser desorption/ionization mass spectrometry(MALDI) or using electron spray mass spectrometry (ESI).

Methods for isolating DNA suitable for these assay technologies areknown in the art. In particular, some embodiments comprise isolation ofnucleic acids as described in U.S. patent application Ser. No.13/470,251 (“Isolation of Nucleic Acids”, published as US 2012/0288868),incorporated herein by reference in its entirety.

In some embodiments, the markers described herein find use in QUARTSassays performed on stool samples. In some embodiments, methods forproducing DNA samples and, in particular, to methods for producing DNAsamples that comprise highly purified, low-abundance nucleic acids in asmall volume (e.g., less than 100, less than 60 microliters) and thatare substantially and/or effectively free of substances that inhibitassays used to test the DNA samples (e.g., PCR, INVADER, QuARTS assays,etc.) are provided. Such DNA samples find use in diagnostic assays thatqualitatively detect the presence of, or quantitatively measure theactivity, expression, or amount of, a gene, a gene variant (e.g., anallele), or a gene modification (e.g., methylation) present in a sampletaken from a patient. For example, some cancers are correlated with thepresence of particular mutant alleles or particular methylation states,and thus detecting and/or quantifying such mutant alleles or methylationstates has predictive value in the diagnosis and treatment of cancer.

Many valuable genetic markers are present in extremely low amounts insamples and many of the events that produce such markers are rare.Consequently, even sensitive detection methods such as PCR require alarge amount of DNA to provide enough of a low-abundance target to meetor supersede the detection threshold of the assay. Moreover, thepresence of even low amounts of inhibitory substances compromise theaccuracy and precision of these assays directed to detecting such lowamounts of a target. Accordingly, provided herein are methods providingthe requisite management of volume and concentration to produce such DNAsamples.

Some biological samples, such as stool samples, contain a wide varietyof different compounds that are inhibitory to PCR. Thus, the DNAextraction procedures include methods to remove and/or inactivate PCRinhibitors. As such, in some embodiments, processing and preparingsamples and particularly, but not exclusively, to methods, systems, andkits for removing assay inhibitors from samples comprising nucleic acidsare described in Example 1.

In some embodiments, the sample comprises blood, serum, plasma, gastricsecretions, pancreatic juice, a gastrointestinal biopsy sample,microdissected cells from a gastrointestinal biopsy, gastrointestinalcells sloughed into the gastrointestinal lumen, and/or gastrointestinalcells recovered from stool. In some embodiments, the subject is human.These samples may originate from the upper gastrointestinal tract, thelower gastrointestinal tract, or comprise cells, tissues, and/orsecretions from both the upper gastrointestinal tract and the lowergastrointestinal tract. The sample may include cells, secretions, ortissues from the liver, bile ducts, pancreas, stomach, colon, rectum,esophagus, small intestine, appendix, duodenum, polyps, gall bladder,anus, and/or peritoneum. In some embodiments, the sample comprisescellular fluid, ascites, urine, feces, pancreatic fluid, fluid obtainedduring endoscopy, blood, mucus, or saliva. In some embodiments, thesample is a stool sample.

Such samples can be obtained by any number of means known in the art,such as will be apparent to the skilled person. For instance, urine andfecal samples are easily attainable, while blood, ascites, serum, orpancreatic fluid samples can be obtained parenterally by using a needleand syringe, for instance. Cell free or substantially cell free samplescan be obtained by subjecting the sample to various techniques known tothose of skill in the art which include, but are not limited to,centrifugation and filtration. Although it is generally preferred thatno invasive techniques are used to obtain the sample, it still may bepreferable to obtain samples such as tissue homogenates, tissuesections, and biopsy specimens. The technology is not limited in themethods used to prepare the samples and provide a nucleic acid fortesting. For example, in some embodiments, a DNA is isolated from astool sample or from blood or from a plasma sample using direct genecapture, e.g., as detailed in U.S. Pat. Nos. 8,808,990 and 9,169,511,and in WO 2012/155072, or by a related method.

The analysis of markers can be carried out separately or simultaneouslywith additional markers within one test sample. For example, severalmarkers can be combined into one test for efficient processing ofmultiple samples and for potentially providing greater diagnostic and/orprognostic accuracy. In addition, one skilled in the art would recognizethe value of testing multiple samples (for example, at successive timepoints) from the same subject. Such testing of serial samples can allowthe identification of changes in marker methylation states over time.Changes in methylation state, as well as the absence of change inmethylation state, can provide useful information about the diseasestatus that includes, but is not limited to, identifying the approximatetime from onset of the event, the presence and amount of salvageabletissue, the appropriateness of drug therapies, the effectiveness ofvarious therapies, and identification of the subject's outcome,including risk of future events.

The analysis of biomarkers can be carried out in a variety of physicalformats. For example, the use of microtiter plates or automation can beused to facilitate the processing of large numbers of test samples.Alternatively, single sample formats could be developed to facilitateimmediate treatment and diagnosis in a timely fashion, for example, inambulatory transport or emergency room settings.

It is contemplated that embodiments of the technology are provided inthe form of a kit. The kits comprise embodiments of the compositions,devices, apparatuses, etc. described herein, and instructions for use ofthe kit. Such instructions describe appropriate methods for preparing ananalyte from a sample, e.g., for collecting a sample and preparing anucleic acid from the sample. Individual components of the kit arepackaged in appropriate containers and packaging (e.g., vials, boxes,blister packs, ampules, jars, bottles, tubes, and the like) and thecomponents are packaged together in an appropriate container (e.g., abox or boxes) for convenient storage, shipping, and/or use by the userof the kit. It is understood that liquid components (e.g., a buffer) maybe provided in a lyophilized form to be reconstituted by the user. Kitsmay include a control or reference for assessing, validating, and/orassuring the performance of the kit. For example, a kit for assaying theamount of a nucleic acid present in a sample may include a controlcomprising a known concentration of the same or another nucleic acid forcomparison and, in some embodiments, a detection reagent (e.g., aprimer) specific for the control nucleic acid. The kits are appropriatefor use in a clinical setting and, in some embodiments, for use in auser's home. The components of a kit, in some embodiments, provide thefunctionalities of a system for preparing a nucleic acid solution from asample. In some embodiments, certain components of the system areprovided by the user.

III. Other Applications

In some embodiments, diagnostic assays identify the presence of adisease or condition in an individual. In some embodiments, the diseaseis cancer (e.g., cancer of the gastrointestinal system).

The present disclosure is not limited to particular markers. In someembodiments, markers whose aberrant methylation is associated with agastrointestinal neoplasm are utilized (e.g., one or more of vimentin,septin 9, NDRG4; see also U.S. Prov. Patent App. No. 62/091,053, filedDec. 12, 2014, which is incorporated by reference herein in itsentirety, for all purposes). In some embodiments, an assay furthercomprises detection of mutated KRAS genes (See e.g., Example 1). In someembodiments, assays further comprise detection of hemoglobin in stoolsamples (See e.g., Example 1).

In some embodiments, the technology relates to a method for treating apatient (e.g., a patient with gastrointestinal cancer, with early stagegastrointestinal cancer, or who may develop gastrointestinal cancer),the method comprising determining the methylation state of one or moremarkers as provided herein and administering a treatment to the patientbased on the results of determining the methylation state. The treatmentmay be administration of a pharmaceutical compound, a vaccine,performing a surgery, imaging the patient, performing another test.Preferably, said use is in a method of clinical screening, a method ofprognosis assessment, a method of monitoring the results of therapy, amethod to identify patients most likely to respond to a particulartherapeutic treatment, a method of imaging a patient or subject, and amethod for drug screening and development.

In some embodiments of the technology, a method for diagnosing agastrointestinal cancer in a subject is provided. The terms “diagnosing”and “diagnosis” as used herein refer to methods by which the skilledartisan can estimate and even determine whether or not a subject issuffering from a given disease or condition or may develop a givendisease or condition in the future. The skilled artisan often makes adiagnosis on the basis of one or more diagnostic indicators, such as forexample a biomarker (e.g., those described herein), the methylationstate of which is indicative of the presence, severity, or absence ofthe condition. Along with diagnosis, clinical cancer prognosis relatesto determining the aggressiveness of the cancer and the likelihood oftumor recurrence to plan the most effective therapy. If a more accurateprognosis can be made or even a potential risk for developing the cancercan be assessed, appropriate therapy, and in some instances less severetherapy for the patient can be chosen. Assessment (e.g., determiningmethylation state) of cancer biomarkers is useful to separate subjectswith good prognosis and/or low risk of developing cancer who will needno therapy or limited therapy from those more likely to develop canceror suffer a recurrence of cancer who might benefit from more intensivetreatments.

As such, “making a diagnosis” or “diagnosing”, as used herein, isfurther inclusive of determining a risk of developing cancer ordetermining a prognosis, which can provide for predicting a clinicaloutcome (with or without medical treatment), selecting an appropriatetreatment (or whether treatment would be effective), or monitoring acurrent treatment and potentially changing the treatment, based on themeasure of the diagnostic biomarkers (e.g., those described herein)disclosed herein. Further, in some embodiments of the presentlydisclosed subject matter, multiple determinations of the biomarkers overtime can be made to facilitate diagnosis and/or prognosis. A temporalchange in the biomarker can be used to predict a clinical outcome,monitor the progression of gastrointestinal cancer, and/or monitor theefficacy of appropriate therapies directed against the cancer. In suchan embodiment for example, one might expect to see a change in themethylation state of one or more biomarkers disclosed herein (andpotentially one or more additional biomarker(s), if monitored) in abiological sample over time during the course of an effective therapy.

The presently disclosed subject matter further provides in someembodiments a method for determining whether to initiate or continueprophylaxis or treatment of a cancer in a subject. In some embodiments,the method comprises providing a series of biological samples over atime period from the subject; analyzing the series of biological samplesto determine a methylation state of at least one biomarker disclosedherein in each of the biological samples; and comparing any measurablechange in the methylation states of one or more of the biomarkers ineach of the biological samples. Any changes in the methylation states ofbiomarkers over the time period can be used to predict risk ofdeveloping cancer, predict clinical outcome, determine whether toinitiate or continue the prophylaxis or therapy of the cancer, andwhether a current therapy is effectively treating the cancer. Forexample, a first time point can be selected prior to initiation of atreatment and a second time point can be selected at some time afterinitiation of the treatment. Methylation states can be measured in eachof the samples taken from different time points and qualitative and/orquantitative differences noted. A change in the methylation states ofthe biomarker levels from the different samples can be correlated withgastrointestinal cancer risk, prognosis, determining treatment efficacy,and/or progression of the cancer in the subject.

In preferred embodiments, the methods and compositions of the inventionare for treatment or diagnosis of disease at an early stage, forexample, before symptoms of the disease appear. In some embodiments, themethods and compositions of the invention are for treatment or diagnosisof disease at a clinical stage.

As noted, in some embodiments, multiple determinations of one or morediagnostic or prognostic biomarkers can be made, and a temporal changein the marker can be used to determine a diagnosis or prognosis. Forexample, a diagnostic marker can be determined at an initial time, andagain at a second time. In such embodiments, an increase in the markerfrom the initial time to the second time can be diagnostic of aparticular type or severity of cancer, or a given prognosis. Likewise, adecrease in the marker from the initial time to the second time can beindicative of a particular type or severity of cancer, or a givenprognosis. Furthermore, the degree of change of one or more markers canbe related to the severity of the cancer and future adverse events. Theskilled artisan will understand that, while in certain embodimentscomparative measurements can be made of the same biomarker at multipletime points, one can also measure a given biomarker at one time point,and a second biomarker at a second time point, and a comparison of thesemarkers can provide diagnostic information.

As used herein, the phrase “determining the prognosis” refers to methodsby which the skilled artisan can predict the course or outcome of acondition in a subject. The term “prognosis” does not refer to theability to predict the course or outcome of a condition with 100%accuracy, or even that a given course or outcome is predictably more orless likely to occur based on the methylation state of a biomarker.Instead, the skilled artisan will understand that the term “prognosis”refers to an increased probability that a certain course or outcome willoccur; that is, that a course or outcome is more likely to occur in asubject exhibiting a given condition, when compared to those individualsnot exhibiting the condition. For example, in individuals not exhibitingthe condition (e.g., having a normal methylation state of one or moretarget genes), the chance of a given outcome (e.g., suffering from agastrointestinal cancer) may be very low. In some embodiments, astatistical analysis associates a prognostic indicator with apredisposition to an adverse outcome. For example, in some embodiments,a methylation state different from that in a normal control sampleobtained from a patient who does not have a cancer can signal that asubject is more likely to suffer from a cancer than subjects with alevel that is more similar to the methylation state in the controlsample, as determined by a level of statistical significance.Additionally, a change in methylation state from a baseline (e.g.,“normal”) level can be reflective of subject prognosis, and the degreeof change in methylation state can be related to the severity of adverseevents. Statistical significance is often determined by comparing two ormore populations and determining a confidence interval and/or a p value.See, e.g., Dowdy and Wearden, Statistics for Research, John Wiley &Sons, New York, 1983, incorporated herein by reference in its entirety.Exemplary confidence intervals of the present subject matter are 90%,95%, 97.5%, 98%, 99%, 99.5%, 99.9% and 99.99%, while exemplary p valuesare 0.1, 0.05, 0.025, 0.02, 0.01, 0.005, 0.001, and 0.0001.

In other embodiments, a threshold degree of change in the methylationstate of a prognostic or diagnostic biomarker disclosed herein can beestablished, and the degree of change in the methylation state of thebiomarker in a biological sample is simply compared to the thresholddegree of change in the methylation state. A preferred threshold changein the methylation state for biomarkers provided herein is about 5%,about 10%, about 15%, about 20%, about 25%, about 30%, about 50%, about75%, about 100%, and about 150%. In yet other embodiments, a “nomogram”can be established, by which a methylation state of a prognostic ordiagnostic indicator (biomarker or combination of biomarkers) isdirectly related to an associated disposition towards a given outcome.The skilled artisan is acquainted with the use of such nomograms torelate two numeric values with the understanding that the uncertainty inthis measurement is the same as the uncertainty in the markerconcentration because individual sample measurements are referenced, notpopulation averages.

In some embodiments, a control sample is analyzed concurrently with thebiological sample, such that the results obtained from the biologicalsample can be compared to the results obtained from the control sample.Additionally, it is contemplated that standard curves can be provided,with which assay results for the biological sample may be compared. Suchstandard curves present methylation states of a biomarker as a functionof assay units, e.g., fluorescent signal intensity, if a fluorescentlabel is used. Using samples taken from multiple donors, standard curvescan be provided for control methylation states of the one or morebiomarkers in normal tissue, as well as for “at-risk” levels of the oneor more biomarkers in tissue taken from donors with metaplasia or fromdonors with a gastrointestinal cancer. In certain embodiments of themethod, a subject is identified as having metaplasia upon identifying anaberrant methylation state of one or more markers provided herein in abiological sample obtained from the subject. In other embodiments of themethod, the detection of an aberrant methylation state of one or more ofsuch biomarkers in a biological sample obtained from the subject resultsin the subject being identified as having cancer.

In some embodiments, the subject is diagnosed as having agastrointestinal cancer if, when compared to a control methylationstate, there is a measurable difference in the methylation state of atleast one biomarker in the sample. Conversely, when no change inmethylation state is identified in the biological sample, the subjectcan be identified as not having gastrointestinal cancer, not being atrisk for the cancer, or as having a low risk of the cancer. In thisregard, subjects having the cancer or risk thereof can be differentiatedfrom subjects having low to substantially no cancer or risk thereof.Those subjects having a risk of developing a gastrointestinal cancer canbe placed on a more intensive and/or regular screening schedule,including endoscopic surveillance. On the other hand, those subjectshaving low to substantially no risk may avoid being subjected to anendoscopy, until such time as a future screening, for example, ascreening conducted in accordance with the present technology, indicatesthat a risk of gastrointestinal cancer has appeared in those subjects.

As mentioned above, depending on the embodiment of the method of thepresent technology, detecting a change in methylation state of the oneor more biomarkers can be a qualitative determination or it can be aquantitative determination. As such, the step of diagnosing a subject ashaving, or at risk of developing, a gastrointestinal cancer indicatesthat certain threshold measurements are made, e.g., the methylationstate of the one or more biomarkers in the biological sample varies froma predetermined control methylation state. In some embodiments of themethod, the control methylation state is any detectable methylationstate of the biomarker. In other embodiments of the method where acontrol sample is tested concurrently with the biological sample, thepredetermined methylation state is the methylation state in the controlsample. In other embodiments of the method, the predeterminedmethylation state is based upon and/or identified by a standard curve.In other embodiments of the method, the predetermined methylation stateis a specifically state or range of state. As such, the predeterminedmethylation state can be chosen, within acceptable limits that will beapparent to those skilled in the art, based in part on the embodiment ofthe method being practiced and the desired specificity, etc.

Further with respect to diagnostic methods, a preferred subject is avertebrate subject. A preferred vertebrate is warm-blooded; a preferredwarm-blooded vertebrate is a mammal. A preferred mammal is mostpreferably a human. As used herein, the term “subject’ includes bothhuman and animal subjects. Thus, veterinary therapeutic uses areprovided herein. As such, the present technology provides for thediagnosis of mammals such as humans, as well as those mammals ofimportance due to being endangered, such as Siberian tigers; of economicimportance, such as animals raised on farms for consumption by humans;and/or animals of social importance to humans, such as animals kept aspets or in zoos. Examples of such animals include but are not limitedto: carnivores such as cats and dogs; swine, including pigs, hogs, andwild boars; ruminants and/or ungulates such as cattle, oxen, sheep,giraffes, deer, goats, bison, and camels; pinnipeds, and horses. Thus,also provided is the diagnosis and treatment of livestock, including,but not limited to, domesticated swine, ruminants, ungulates, horses(including race horses), and the like. The presently-disclosed subjectmatter further includes a system for diagnosing a gastrointestinalcancer in a subject. The system can be provided, for example, as acommercial kit that can be used to screen for a risk of gastrointestinalcancer or diagnose a gastrointestinal cancer in a subject from whom abiological sample has been collected. An exemplary system provided inaccordance with the present technology includes assessing themethylation state of a marker described herein.

Over recent years, it has become apparent that circulating epithelialcells, representing metastatic tumor cells, can be detected in the bloodof many patients with cancer. Molecular profiling of rare cells isimportant in biological and clinical studies. Applications range fromcharacterization of circulating epithelial cells (CEpCs) in theperipheral blood of cancer patients for disease prognosis andpersonalized treatment (See e.g., Cristofanilli M, et al. (2004) N EnglJ Med 351:781-791; Hayes D F, et al. (2006) Clin Cancer Res12:4218-4224; Budd G T, et al. (2006) Clin Cancer Res 12:6403-6409;Moreno J G, et al. (2005) Urology 65:713-718; Pantel et al., (2008) NatRev 8:329-340; and Cohen S J, et al. (2008) J Clin Oncol 26:3213-3221).

Experiments conducted during the course of development of embodiments ofthe present disclosure identified the unexpected result that thepresence of methylated ZDHHC1 in blood or plasma is correlated with thepresence of epithelial cells in blood in patients with metastaticcancer. Accordingly, embodiments of the present disclosure providecompositions and methods for detecting the presence of metastatic cancerin a subject by identifying the presence of methylated ZDHHC1 in plasmaor whole blood. The presence of methylated ZDHHC1 is identified usingany suitable method (e.g., those described herein).

EXPERIMENTAL EXAMPLES Example 1 Methods for DNA Isolation and QUARTSAssay

The following provides exemplary method for DNA isolation prior toanalysis, and an exemplary QUARTS assay, such as may be used inaccordance with embodiments of the technology. Application of QuARTStechnology to DNA from stool and various tissue samples is described inthis example, but the technology is readily applied to other nucleicacid samples, e.g., as shown in other examples.

Collection of Target DNA from Stool Samples.

Whole stools are collected in plastic buckets. A preservative buffer,e.g., 150 mM EDTA, 500 mM Tris-Cl and 10 mM NaCl, (pH 9.0) is added tothe stool, e.g., at about 4 ml per gram of stool, and buffered stoolsmay be used directly or archived at −80° C.

Exemplary procedure for isolation of target nucleic acids from stoolsamples:

-   -   1. A stool sample is homogenized, e.g., with a buffer, to form a        stool homogenate. The homogenate treated to partition residual        solids from the fluid, e.g., by centrifugation or filtration, to        produce a “stool supernatant.”    -   2. Stool supernatant is treated to remove assay inhibitors        (e.g., with polyvinylpolypyrrolidone, as described in U.S. Pat.        No. 8,993,341, which is incorporated herein by reference in its        entirety), producing “clarified supernatant”.    -   3. Ten milliliters of clarified supernatant (representing an        equivalent of approximately 4 grams of stool) is mixed with        guanidine thiocyanate (GTC) to a final concentration of 2.4 M;    -   4. The mixture is then heated in a 90° C. water bath for 10        minutes to denature the DNA (and proteins) present in the stool.    -   5. Paramagnetic particles containing covalently attached        (coupled) oligonucleotides complementary to the target        sequence(s) of interest (“target-specific capture probes”) are        added to the sample. The sample is then incubated (e.g., at        ambient temperature, about 22-25° C.) for one hour to enable        hybridization of the target DNA to the capture probes on the        magnetic particles.    -   6. The mixture of clarified supernatant, GTC, and particles is        exposed to a magnetic field to separate the particles (now        containing target DNA hybridized to the capture probes) from the        stool supernatant/GTC mixture, which is transferred to a new        tube. See, e.g., U.S. patent application Ser. No. 13/089,116,        which is incorporated herein by reference.

The denaturation/hybridization/separation cycle (steps 4-6) can berepeated, e.g., least four or more times to serially extract differenttarget DNAs from the same stool supernatant sample.

FFPE Tissue DNA

DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is isolatedusing the QIAamp DNA FFPE Tissue Kit (Qiagen Sciences, Germantown, Md.).

DNA Isolation from Cells and Plasma

For cell lines, genomic DNA may be isolated from cell conditioned mediausing, for example, the “Maxwell® RSC ccfDNA Plasma Kit (Promega Corp.,Madison, Wis.). Following the kit protocol, 1 mL of cell conditionedmedia (CCM) is used in place of plasma, and processed according to thekit procedure.

An exemplary procedure for isolating DNA from a 4 mL sample of plasma isas follows:

-   -   To a 4 mL sample of plasma, 300 μL of Proteinase K (20 mg/mL) is        added and mixed.    -   Add 3 μL of 1 μg/μL of Fish DNA to the plasma-proteinase K        mixture.    -   Add 2 mL of plasma lysis buffer to plasma.        -   Plasma lysis buffer is:            -   4.3M guanidine thiocyanate            -   10% IGEPAL CA-630 (Octylphenoxy                poly(ethyleneoxy)ethanol, branched)            -   (5.3 g of IGEPAL CA-630 combined with 45 mL of 4.8 M                guanidine thiocyanate)    -   Incubate mixtures at 55° C. for 1 hour with shaking at 500 rpm.    -   Add 3 mL of plasma lysis buffer and mix.    -   Add 200 μL magnetic silica binding beads [16 μg of beads/μL] and        mix again.    -   Add 2 mL of 100% isopropanol and mix.    -   Incubate at 30° C. for 30 minutes with shaking at 500 rpm.    -   Place tube(s) on magnet and let the beads collect. Aspirate and        discard the supernatant.    -   Add 750 μL GuHCl-EtOH to vessel containing the binding beads and        mix.        -   GuHCl EtOH wash buffer is:            -   3M GuHCl            -   57%9 EtOH.    -   Shake at 400 rpm for 1 minute.    -   Transfer samples to a deep well plate or 2 mL microfuge tubes.    -   Place tubes on magnet and let the beads collect for 10 minutes.        Aspirate and discard the supernatant.    -   Add 1000 μL wash buffer (10 mM Tris HCl, 80% EtOH) to the beads,        and incubate at 30° C. for 3 minutes with shaking.    -   Place tubes on magnet and let the beads collect. Aspirate and        discard the supernatant    -   Add 500 μL, wash buffer to the beads and incubate at 30° C. for        3 minutes with shaking.    -   Place tubes on magnet and let the beads collect. Aspirate and        discard the supernatant.    -   Add 250 μL, wash buffer and incubate at 30° C. for 3 minutes        with shaking.    -   Place tubes on magnet and let the beads collect. Aspirate and        discard the remaining buffer.    -   Add 250 μL, wash buffer and incubate at 30° C. for 3 minutes        with shaking.    -   Place tubes on magnet and let the beads collect. Aspirate and        discard the remaining buffer.    -   Dry the beads at 70° C. for 15 minutes, with shaking.    -   Add 125 μL, elution buffer (10 Tris HCl, pH 8.0, 0.1 mM EDTA) to        the beads and incubate at 65° C. for 25 minutes with shaking.    -   Place tubes on magnet and let the beads collect for 10 minutes.    -   Aspirate and transfer the supernatant containing the DNA to a        new vessel or tube.

QuARTS Assay

The QuARTS technology combines a polymerase-based target DNAamplification process with an invasive cleavage-based signalamplification process. The technology is described, e.g., in U.S. Pat.Nos. 8,361,720; 8,715,937; 8,916,344; and U.S. patent application Ser.Nos. 14/036,649, each of which is incorporated herein by reference.Fluorescence signal generated by the QuARTS reaction is monitored in afashion similar to real-time PCR and permits quantitation of the amountof a target nucleic acid in a sample.

An exemplary QuARTS reaction typically comprises approximately 400-600nmol/1 (e.g., 500 nmol/1) of each primer and detection probe,approximately 100 nmol/1 of the invasive oligonucleotide, approximately600-700 nmol/1 of each FRET cassette (FAM, e.g., as suppliedcommercially by Hologic, Inc.; HEX, e.g., as supplied commercially byBioSearch Technologies, IDT; and Quasar 670, e.g., as suppliedcommercially by BioSearch Technologies), 6.675 ng/μl FEN-1 endonuclease(e.g., Cleavase® 2.0, Hologic, Inc.), 1 unit Taq DNA polymerase in a 30μl reaction volume (e.g., GoTaq® DNA polymerase, Promega Corp., Madison,Wis.), 10 mmol/l 3-(n-morpholino) propanesulfonic acid (MOPS), 7.5mmol/l MgCl₂, and 250 μmol/l of each dNTP. Exemplary QuARTS cyclingconditions consist of an initial incubation at 95° C. for 3 minutes,followed by 10 cycles of 95° C. for 20 seconds, 67° C. for 30 seconds,and 70° C. for 30 seconds. After completion of the 10 cycles, anadditional 37 cycles at 95° C. for 20 seconds, 53° C. for 1 minute, 70°C. for 30 seconds, and 40° C. for 30 seconds are typically performed. Insome applications, analysis of the quantification cycle (C_(q)) providesa measure of the initial number of target DNA strands (e.g., copynumber) in the sample.

For stool DNA testing, capture probes are generally used as describedabove to capture target nucleic acid fragments from clarifiedsupernatants, as discussed above. Examples of capture probes are shownbelow, and typically comprise a 5′-six carbon amino modified linkage(Integrated DNA Technology, Coralville, Iowa):

for NDRG4: (SEQ ID NO: 1)/5AmMC6/TCCCTCGCGCGTGGCTTCCGCCTTCTGCGCGGCTGGGGTG CCCGGTGG-3′ for BMP3:(SEQ ID NO: 2) /5AmMC6/GCGGGACACTCCGAAGGCGCAAGGAG-3′ for KRAS:(SEQ ID NO: 3) /5AmMC6/GGCCTGCTGAAAATGACTGAATATAAACTTGTGGTAGTTGGAGC-3′ and (SEQ ID NO: 4)/5AmMC6/CTCTATTGTTGGATCATATTCGTCCACAAAATGATTCTGA ATTAGC-3′

Captured DNA for methylation testing is treated with bisulfite using,e.g., the EZ-96 DNA Methylation Kit (Zymo Research, Irvine Calif.) orusing ammonium hydrogen sulfite as described in WO 2013/116375,incorporated herein by reference. The converted sample is typicallyeluted in 50 microliters of 10 mM Tris, 0.1 mM EDTA pH 8.0 with 20nanograms per microliter tRNA (Sigma); 10 microliters ofbisulfite-treated DNA are assayed with the QuARTS method in30-microliter reaction volumes on a 96-well PCR plate. PCR plates arecycled in a LightCycler 480 (Roche).

QuARTS assays may be directed to individual markers or multiplexedcombinations of markers, and typically additionally compriseoligonucleotides for detection of a reference nucleic acid, e.g.,β-actin, or the markers discussed in embodiments of the invention,below.

In this embodiment, for each target below, the primers and probe(Integrated DNA Technology, Coralville, Iowa) are as follows:

for NDRG4: (SEQ ID NO: 5) Primer 5′-CGG TTT TCG TTC GTT TTT TCG-3′,(SEQ ID NO: 6) Primer 5′-GTA ACT TCC GCC TTC TAC GC-3′, (SEQ ID NO: 7)Probe 5′-CGC CGA GGG TTC GTT TAT CG/3′C6/ for BMP3: (SEQ ID NO: 8)Primer 5′-GTT TAA TTT TCG GTT TCG TCG TC-3′ (SEQ ID NO: 9) Primer5′-CTC CCG ACG TCG CTA CG-3′ (SEQ ID NO: 10) Probe5′-CGC CGA GGC GGT TTT TTG CG/3′C6/ For bisulfite-treated β-actin:(SEQ ID NO: 52) Primer 5′-TTT GTT TTT TTG ATT AGG TGT TTA AGA-3′(SEQ ID NO: 59) Primer 5′-CAC CAA CCT CAT AAC CTT ATC-3′ (SEQ ID NO: 60)Probe 5′-CCA CGG ACG ATA GTG TTG TGG/3′C6/

Each assay, e.g., in an assay plate, includes bisulfite-treated DNAsamples, standard curve samples, positive and negative controls.Standard curves are may be made using target strands cut from engineeredplasmids, e.g., at 300 to 1000 strands. Bisulfite-treated CpGenomeuniversal methylated DNA (Millipore, Billerica, Mass.) and human genomicDNA (Merck, Germany) are used as positive and negative controls. DNAstrand number is determined by comparing the C_(p) of the target gene tothe standard curve for the relevant assay. Percent methylation for eachmarker is determined by dividing the strand number of the methylatedgene by the control DNA (e.g., β-actin, or the candidate control markersprovided herein) strand number and multiplying by 100.

KRAS Mutations

QuARTS assays are used to evaluate seven mutations at codons 12/13 ofthe KRAS gene. Each mutation assay is designed as a singleplex assay.KRAS mutation-specific forward primers and probes are:

for G12S mutation: (SEQ ID NO: 11) Primer5′-CTT GTG GTA GTT GGA GCA A-3′ (SEQ ID NO: 12) Probe5′-GCG CGT CCA GTG GCG TAG GC/3′C6/; for G12C mutation (SEQ ID NO: 13)Primer 5′-AAA CTT GTG GTA GTT GGA CCT T-3′ (SEQ ID NO: 14) Probe5′-GCG CGT CCT GTG GCG TAG GC/3′C6/; for G12R mutation (SEQ ID NO: 15)Primer 5′-TAT AAA CTT GTG GTA GTT GGA CCT C-3′ (SEQ ID NO: 16) Probe5′-GCG CGT CCC GTG GCG TAG GC/3′C6/; for G12D mutation (SEQ ID NO: 17)Primer 5′-ACT TGT GGT AGT TGG AGC TCA-3′ (SEQ ID NO: 18) Probe5′-GCG CGT CCA TGG CGT AGG CA/3′C6/; for G12V mutation (SEQ ID NO: 19)Primer 5′-ACT TGT GGT AGT TGG AGC TCT-3′ (SEQ ID NO: 20) Probe5′-GCG CGT CCT TGG CGT AGG CA/3′C6/; for G12A mutation (SEQ ID NO: 21)Primer 5′-AAC TTG TGG TAG TTG GAG ATG C-3′ (SEQ ID NO: 22) Probe5′-GCG CGT CCC TGG CGT AGG CA/3′C6/; for G13D mutation (SEQ ID NO: 23)Primer 5′-GGT AGT TGG AGC TGG TCA-3′ (SEQ ID NO: 24) Probe5′-GCG CGT CCA CGT AGG CAA GA/3′C6/For all KRAS mutants, the reverse primer used is (SEQ ID NO: 25)5′-CTA TTG TTG GAT CAT ATT CGT C-3′

QuARTS cycling conditions and reagent concentrations for KRAS are thesame as those in the methylation assays. Each plate contains standardsmade of engineered plasmids, positive and negative controls, and waterblanks, and is run in a LightCycler 480 (Roche) or ABI 7500 (ThermoScientific). DNA strand number is determined by comparing the C_(p) orC_(T) of the target gene to the standard curve for that assay. Theconcentration of each mutation marker in 50 microliters of KRAS iscalculated based on the 500-fold dilution factor and an amplificationefficiency of 1.95. This value is divided by the β-actin concentrationor the ZDHHC1 in the methylation assay and then multiplied by 100 todetermine the percent mutation.

In the assays discussed below, “BTACT” refers to characterization ofβ-actin in the methylation assay and “ACT” or “ACTB” refers tocharacterization of β-actin in the mutation assay.

Example 2 Identification and Testing of Candidate Control Genes

As discussed above, in certain embodiments, control genes of thetechnology are selected according to methylation state. In a first step,genes that are highly methylated in both normal and cancer epithelialtissue cells are selected as candidate control genes. As a second step,the selected candidate genes are screened to identify genes wherein themethylated form of the gene is minimally present in blood and bloodfractions. In preferred embodiments, candidate genes may be furtheranalyzed to select genes having a GC-content and CpG methylation contentsimilar to one or more marker gene(s) to be analyzed, such thatbisulfite reactivity and PCR amplification behaviors are similar to themarker gene(s) to be analyzed.

ZDHHC1, ZFAND3, ZMYM4, ODZ2, and TRIO were identified as methylatedgenes possibly suitable for use as controls.

These candidate markers have the following loci (referenced toGRCh37/hg19 assembly):

ZDHHC1 footprint: Chr 16, 67428559-67428628

ZMYM4 footprint: Chr 1, 35877002-35877078

ZFAND3 footprint: Chr 6, 37841985-37842061

ODZ2 footprint: Chr 5, 167285650-167285775

TRIO footprint: Chr 5, 14461291-14461417

ZDHHC1, ZFAND3, and ZMYM4 genes were selected for further analysis andwere assayed using QuARTS technology to compare methylation of the genesin the normal and cancer samples, and to assess presence of the markersin blood (e.g., in serum). The oligonucleotides used in the assays areshown schematically below. The term “wild type” is used to refer to thesequence of the genes in the absence of bisulfite conversion, which isnot affected by methylation state.

ZDHHC1—Zinc Finger, DHHC-Type Containing 1

Untreated Target Sequence: (SEQ ID NO: 26)5'-GGGGCCGGGGCCGACAGCCCACGCTGGCGCGGCAGGCGCGTGCGCCCGCCGTTTTCGTGAGCCCGAGCAG-3′Bisulfite-treated Target Sequence: (SEQ ID NO: 33)5′-GGGGUCGGGGUCGAUAGUUUACGUTGGCGCGGUAGGCGCGTGCGUUCGUCGTTTTCGTGAGUUCGAGUAG-3′Bisulfite-treated, replicated Target Sequence: (SEQ ID NO: 27)5′-GGGGTCGGGGTCGATAGTTTACGTTGGCGCGGTAGGCGCGTGCGTTCGTCGTTTTCGTGAGTTCGAGTAG-3′QuARTS Assay Design 1: (SEQ ID NO: 28)             5′ Arm-3-GTTGGCGCGGTA-3                       ||||||||||||                  (SEQ ID NO: 27)GGGGTCGGGGTCGATAGTTTACGTTGGCGCGGTAGGCGCGTGCGTTCGTCGTTTTCGTGAGTTCGAGTAG-3′   ||||||||||||||||||||                      ::::::::::::::::::::5′-GTCGGGGTCGATAGTTTACG>>                  <<AGCAGCAAAAGCACTCAAGC-5′     (SEQ ID NO: 29)                           (SEQ ID NO: 30)QuARTS Assay Design 2 (v3):                                     (SEQ ID NO: 31)                                    GCACGCAAGCAG-Arm3-5′       (SEQ ID NO: 27)                ::::::::::::GGGGTCGGGGTCGATAGTTTACGTTGGCGCGGTAGGCGCGTGCGTTCGTCGTTTTCGTGAGTTCGAGTAG   ||||||||||||||||||||                          :::::::::::::::::::   GTCGGGGTCGATAGTTTACG>>                      <<GCAAAAGCACTCAAGCTCA    (SEQ ID NO: 29)                                (SEQ ID NO: 32)

QuARTS Assay Oligonucleotides (all Shown 5′ to 3′):

ZDHHC1 FP GTCGGGGTCGATAGTTTACG SEQ ID NO: 29 ZDHHC1 RPCGAACTCACGAAAACGACGA SEQ ID NO: 30 ZDHHC1 GACGCGGAG GTTGGCGCGGTA/SEQ ID NO: 34 Probe A3 3C6/ ZDHHC1 ACTCGAACTCACGAAAACG SEQ ID NO: 32RP_v3 ZDHHC1 GACGCGGAG-GACGAACGCACG/ SEQ ID NO: 35 ProbeA3_v3 3C6/ZDHHC1 CP /5amm6/CTCGGGCTCACGAAAA SEQ ID NO: 36 Prb CGGCGGGCGCAC

ZFAND3—Zinc Finger, AN1-Type Domain 3

Untreated Target Sequence: (SEQ ID NO: 37)5′-TCTCTGTGTACTAATTTCCCTTTTTGGCCGGACGTGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAAG-3′Bisulfite-treated Target Sequence: (SEQ ID NO: 38)5′-TTTTTGTGTATTAATTTTTTTTTTTGGTCGGACGTGGTGGTTTACGTTTGTAATTTTAGTATTTTGGGAGGTTAAAG-3′QuARTS Assay Design:    (SEQ ID NO: 39)                       5′Arm-3-ACGTGGTGGTTT -3′                               ||||||||||||             (SEQ ID NO: 38)TTTTTGTGTATTAATTTTTTTTTTTGGTCGGACGTGGTGGTTTACGTTTGTAATTTTAGTATTTTGGGAGGTTAAAG    ||||||||||||||||||||||||||||           :::::::::::::::::::::::::::: 5′-TGTGTATTAATTTTTTTTTTTGGTCGGA>>       <<TGCAAACATTAAAATCATAAAACCCTCC-5′           (SEQ ID NO: 40)                       (SEQ ID NO: 41)

QuARTS Assay Oligonucleotides (all Shown 5′ to 3′):

ZFAND3 TGTGTATTAATTTTTTTTTTTGGTCGGA SEQ ID FP NO: 40 ZFAND3CCTCCCAAAATACTAAAATTACAAACGT SEQ ID RP NO: 41 ZFAND3GACGCGGAG ACGTGGTGGTTT /3C6/ SEQ ID Probe A3 NO: 42 ZFAND3/5amm6/GTGCTGGGATTACAGGCGTGA SEQ ID CP Prb GCCACCACGTCCGG NO: 43

ZMYM4—Zinc Finger, MYM-Type 4

Untreated Target Sequence: (SEQ ID NO: 44)5′-CCATCTATAGAAAAATGGATTAGGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCA-3′Bisulfite-treated Target Sequence: (SEQ ID NO: 45)5′-TTATTTATAGAAAAATGGATTAGGGTCGGGTATAGTGGTTTACGTTTGTAATTTTAGTATTTTGGGAGGTCGAGGTA-3′QuARTS Assay Design:             (SEQ ID NO: 46)                               3′-CACCAAATGCAA-Arm-3-5′                                  ::::::::::::             (SEQ ID NO: 45)TTATTTATAGAAAAATGGATTAGGGTCGGGTATAGTGGTTTACGTTTGTAATTTTAGTATTTTGGGAGGTCGAGGTA         ||||||||||||||||||||||              ::::::::::::::::::::::::::::      5′-GAAAAATGGATTAGGGTCGGGT>>          <<AACATTAAAATCATAAAACCCTCCAGCT-5′             (SEQ ID NO: 47)                        (SEQ ID NO: 48)

QuARTS Assay Oligonucleotides (all Shown 5′ to 3′):

ZMYM4 GAAAAATGGATTAGGGTCGGGT SEQ ID NO: 47 FP v2 ZMYM4TCGACCTCCCAAAATACTAAAATTA SEQ ID NO: 48 RP v2 CAA ZMYM4GACGCGGAG AACGTAAACCAC/ SEQ ID NO: 49 Probe 3C6/ A3 v2 ZMYM4/5amm6/CGGCCTCCCAAAGTGCTG SEQ ID NO: 50 CP Prb GGATTACAGGCGTGAGCC

Quasar 670 A3 FRET Cassette: (SEQ ID NO: 51)5′ d Q670-TCT(I-BHQ2)AGCCGGTTTTCCGGCTGAGACTCCGCG TC-C6 3′FP = forward primer; RP =reverse primer;3′ C6 =3′ hexane; 5amm6 = 5′ amino; CP = capture probe; Q670 = Quasar ®670 dye; BHQ2 = Black Hole Quencher 2]

Using the oligonucleotide combinations described above, methylationanalysis of cancer markers NDRG4 and BMP3 was performed on a variety ofdifferent sample types (blood, plasma, and two human colorectal cancercell lines, HT29 and HT116) using β-actin (BTACT) for normalization, orusing one of the three candidate control genes (ZDHHC1, ZMYM, and ZFAND)for normalization. Assays were performed in duplicate as described inExample 1. Table 1 shows the averages of the replicates:

TABLE 1 Average Strands SampleID NDRG4 BMP3 BTACT ZDHHC1 ZFAND3 ZMYM4v2Blood 0 8 18160 0 41136 42905175 Plasma 0 0 1 0 15 9382 HT29 66008 64728114720 141602 106223 36106311 HT116 75394 59933 114944 257075 11287335033276

It can be seen from these data that all three candidate markers, likeBTACT, show strong positive signal in cancer cell lines HT29 and HT116.However, both ZFAND3 and ZMYM4v2, like BTACT, show significant signal inblood samples, such as can produce undesirable background in sampleshaving an amount of blood present, e.g., tissue or stool samples.

This example shows that ZDHHC1 has lower background signal in blood andplasma, and that it is readily detected in epithelial cell lines. ZDHHC1was selected for further analysis.

Example 3 Comparing β Actin and ZDHHC1 for Normalizing Cancer MarkerAssays

The ZDHHC1 marker was tested in parallel with BTACT, to compare theseDNAs as controls for determining % methylation of the NDRG4 and BMP3marker genes. DNA isolated from formalin-fixed, paraffin-embedded tissuesamples was characterized, with assay signals normalized to β-actin orZDHHC1. The results are shown in Table 3, below.

These data show that % methylation of the NDRG4 and BMP3 markersrelative to ZDHHC1 is comparable to % methylation of the same markersrelative to β-actin, showing that ZDHHC1 may be used in place of β-actinfor normalizing.

TABLE 3 Strands normalized to % Methylation Strands normalized to %Methylation ZDHHC1 relative to ZDHHC1 BTACT relative to BTACT SampleIDNDRG4 BMP3 ZDHHC1 % NDRG4 % BMP3 NDRG4 BMP3 BTACT % NDRG4 % BMP3 683(1:5) 31 0 123 25.5 0.0 99 0 356 27.8 0.0 538 (1:5) 625 504 563 111.089.4 2413 1559 3739 64.5 41.7 536 (1:5) 1126 0 1105 101.9 0.0 3737 03421 109.2 0.0 279 (1:5) 365 518 899 40.6 57.6 3935 4671 11449 34.4 40.8544 (1:5) 4739 1159 3684 128.6 31.5 44858 17705 41324 108.6 42.8 602(1:5) 238 22 5533 4.3 0.4 3784 163 67690 5.6 0.2 654 (1:5) 43 4 1067 4.00.4 965 25 20833 4.6 0.1 686 (1:5) 198 168 985 20.1 17.1 1077 1140 195755.0 58.3 160 (1:5) 1347 784 2095 64.3 37.4 45346 36657 85629 53.0 42.8309 (1:5) 0 3 7039 0.0 0.0 0 8 65247 0.0 0.0 602 (1:5) 130 19 3133 4.20.6 3784 163 67690 5.6 0.2 131 66 41 135 49.2 30.5 169 92 336 50.3 27.4669 167 201 592 28.2 34.0 271 235 744 36.4 31.6 681 932 815 567 164.4143.7 822 745 464 177.2 160.6 673 0 0 171 0.0 0.0 0 0 145 0.0 0.0

As shown in Table 3, comparison of the % methylation values determinedusing ZDHHC1 and using BTACT shows that these controls are equivalent inperformance on these tissue samples, and that ZDHHC1 may be used inplace of BTACT in measuring methylation of the cancer marker genes.

Example 4 ZDHHC1 and 11-Actin DNA in Normal and Cancer Tissue Samples

This example describes a comparison of the number of ZDHHC1 and β-actinstrands in an extended sampling of different cancerous and normal tissuesamples. DNA from normal and abnormal tissue types, including bile duct,colon, esophageal, head, lung, pancreas, small bowel, and stomach, weretested.

DNA isolated from formalin-fixed, paraffin-embedded tissue samples wascharacterized, with median assay signals for β-actin (ACTB) and ZDHHC1shown in Table 4, below.

TABLE 4 Median Median Tissue/disease (ZDHHC1 strands) (ACTB strands(WT)) Bile duct/ACA 2500.5 7470 Bile duct/normal 2516.5 12300 Colon/ACA1229.5 32883.5 Colon/adenoma-ge-1 cm 865 20409.5 Colon/HGD 1423 15210Colon/normal 355.5 7666 Colon/SSP 1255.5 11268 Esophagus/cancer 506Esophagus/normal 648 Esophagus/adenocarcinoma 735 4760 Esophagus/SCC1258 20950 Head/oropharyng. 279 23158.5 Lung/large airway 201 4330Pancreas/ACA 1345 Pancreas/normal 1397.5 Small bowel/ACA 609.5 17767Small bowel/adenoma 543 11936.5 Stomach/ACA 642 14826 Stomach/adenoma465 20164 Stomach/metaplasia 1238 10695 Stomach/normal 220.5 10555.5

These data confirm that the methylated ZDHHC1 control is detected in alltissue types tested, and in normal and non-normal (e.g., adenoma,carcinoma, metaplasia) tissue types. Results show equal ZDHHC1methylation between cancer and normal tissues.

Example 5 Effect of ZDHHC1 for Normalizing Cancer Marker Assays inComplex Samples

Further experiments were conducted on the use of ZDHHC1 as a normalizingmarker in assays to detect cancer in more complex samples, e.g., stool,blood, etc., and in normal and colorectal cancer tissue samples. Table5A shows the strands detected of the NDRG4 methylation marker and forboth control DNAs, and shows the % methylation of NDRG4 as determinedusing each control DNA. Data for the BMP3 marker detected in the sameassay reactions in shown in Table 5B.

TABLE 5A Marker % NDRG4 Methylation Gene Control Gene calculated fromStrands Strands each control DNA Sample ID NDRG4 BTACT ZDHHC1 BTACTZDHHC1 Stool Pool 596 4825 3589 12.35 16.61 CRC POS Stool Pool 569 39063441 14.56 16.53 CRC POS Stool Pool 25 3349 4630 0.74 0.53 NORM StoolPool 32 3762 3943 0.85 0.81 NORM Blood 0 16036 16 0 0 Blood 0 17970 0 00 Cell Lines HT29 73418 111915 123115 65.60 59.63 HT116 84758 106098148448 79.89 57.10 Colorectal Cancer Positive Tissue Samples a489 8551946 3057 43.91 27.96 620 334 913 3148 36.55 10.60 4229 0 1801 2502 0 04247 278 1347 1255 20.65 22.17 Normal Tissue Samples 1233402220 0 13981772 0 0 1233402240 0 1065 1811 0 0 1233402253 0 1227 1859 0 0

TABLE 5B Marker % BMP3 Methylation Gene Control Gene calculated fromStrands Strands each control DNA Sample ID BMP3 BTACT ZDHHC1 BTACTZDHHC1 Stool Pool 161 4825 3589 3.34 4.49 CRC POS Stool Pool 149 39063441 3.80 4.32 CRC POS Stool Pool 5 3349 4630 0.16 0.12 NORM Stool Pool6 3762 3943 0.17 0.16 NORM Blood 2 16036 16 0.01 9.71 Blood 1 17970 00.01 0 Cell Lines HT29 72886 111915 123115 65.13 59.20 HT116 66605106098 148448 62.78 44.87 Colorectal Cancer Positive Tissue Samples a4890 1946 3057 0 0 620 0 913 3148 0 0 4229 0 1801 2502 0 0 4247 189 13471255 14.00 15.03 Normal Tissue Samples 1233402220 0 1398 1772 0.03 0.021233402240 1 1065 1811 0.05 0.03 1233402253 0 1227 1859 0 0These data show that the methylated ZDHHC1 control DNA presence isessentially uniform in stool samples from both normal and colorectalcancer-positive subjects, and confirm that the marker is substantiallyabsent in blood samples. These data also confirm that ZDHHC1 presence isessentially equivalent to β-actin DNA samples that do not contain blood(e.g., cell lines).

Example 6 ZDHHC1 in Plasma Samples of Subjects with Metastatic Cancer

This example described detection of ZDHHC1 in plasma samples of patientswith metastatic cancer.

One to two milliliter samples of normal, advanced adenoma (AA) andadenocarcinoma (ACA), patient plasma were used in QUARTS assays. Plasmasamples from colon cancer subjects and normal subjects were processedusing Qiagen Circulating Nucleic Acid Kit. Starting volumes of plasmaranged from 0.75-2.0 ml. DNA was bisulfite-converted and tested withZDHHC1 and the BTACT oligo mixtures. Results show that ZDHHC1 strandlevels were high in the stage IV cancer sample with liver metastasis.

All samples, except one, had no ZDHHC1 marker strands. The one samplethat showed large number of strands for ZDHHC1 marker in plasma is astage IV metastases. These data support the use of ZDHHC1 to detectepithelial cells in blood/plasma as a general marker for metastasis.Results are summarized in the Table 6:

TABLE 6 Avg. Avg. Avg. BTACT ZDHHC Z/BTACT Type Number strands strands %Normal 8 481 4 1 AA 4 193 3 2 ACA, stage I* 3 104 1 1 ACA, stage II 6264 6 2.3 ACA, stage III 2 200 10 50 ACA, stage IV, 1 2325 3998 172w/mets *includes one sample not characterized by stage.In an additional study of two AA samples, eight ACA samples, of whichtwo were classed as stage IV with observed metastases, and 34 normalsamples, one of the stage IV was detected, displaying a significantlyelevated ratio of ZDHHC1 BTACT (41%) and one appeared to have normalratio of ZDHHC1/BTACT(4.3%). None of the other samples displayed anelevated ratio of ZDHHC1 BTACT.

Example 7 ZDHHC1 in Plasma Samples of Subjects with Cancer

Plasma levels for ZDHHC1 were measured on an additional set of patientsamples comprising 57 samples from patients with cancer and 52 normalsamples, as detailed in FIGS. 4A-4E. DNA was extracted from 4 ml ofplasma and bisulfate-converted. The ZDHHC1 DNA was pre-amplified for 10cycles then detected using a QuARTS flap assay as described in Example1, using the primers and probes described in Example 2. The results areshown in the table in FIGS. 4A-4E, and the averaged data for each sampletype is as follows:

Sample Diagnosis ZDHHC1 copies Plasma Normal Colonoscopy Avg Copies = 11Plasma Panc Cancer Avg Copies = 1,041 Plasma Small Bowel Cancer AvgCopies = 12,001 (1 Sample) Plasma Lung Cancer Avg Copies = 300 PlasmaColorectal Cancer Avg Copies = 459

Example 8 Detection of ZDHHC1 for Monitoring Disease State and/orProgression

Patient samples, e.g., blood product samples such as plasma samples, maybe analyzed for the presence of epithelial cells or epithelial cell DNAas means of monitoring a disease state, e.g., occurrence, progression,response to therapy, post-surgery, remission, recurrence, etc. In someembodiments, samples are taken from a patient at multiple time pointsand the amount of ZDHHC1 DNA present (whether free or in circulatingcells or complexes) is measured at each time point, and the amounts ofZDHHC1 DNA in the samples taken at the different time points arecompared to assess changes in the disease state.

At a first time point, a sample of blood is taken from a patient and aplasma sample is prepared.

At a second time point, a second sample of blood is taken from thepatient and a second plasma sample is prepared.

Either the entire blood sample is tested for ZDHHC1 DNA or the sample isfurther processed to yield a plasma fraction.

Each plasma sample is tested for the presence and amount of ZDHHC1 DNA,e.g., using methods as described in Example 1 and 6, above. It iscontemplated that, in some embodiments, the first sample is notimmediately tested (e.g., the blood or the plasma, or DNA isolatedtherefrom, is stored for later testing) and the first and second samplesare tested at the same time. In other embodiments, the first plasmasample is tested prior to the collection of the second blood sample, andthe results are stored for later comparison.

The technology is not limited to a particular event or course of actionoccurring between the first and second time points. For example, thefirst time point may be at a time where there is no suspicion ofdisease, e.g., the first assay may be to establish a baseline in theexpectation of monitoring the subject for future disease occurrence.Alternatively, the first time point may be taken at a point at which acondition or disease may be present in the subject, but the diseasestate is one for which monitoring is preferred over active therapeuticintervention as a course of action, e.g., the disease state may bemonitored for changes such as metastases. In other situations, activetherapy, e.g., surgery, drug therapy, etc., may be administered to thesubject between the two time points, and the measurement of epithelialcell DNA in the blood may be used to monitor efficacy of the therapy.

All publications and patents mentioned in the above specification areherein incorporated by reference in their entirety for all purposes.Various modifications and variations of the described compositions,methods, and uses of the technology will be apparent to those skilled inthe art without departing from the scope and spirit of the technology asdescribed. Although the technology has been described in connection withspecific exemplary embodiments, it should be understood that theinvention as claimed should not be unduly limited to such specificembodiments. Indeed, various modifications of the described modes forcarrying out the invention that are obvious to those skilled inpharmacology, biochemistry, medical science, or related fields areintended to be within the scope of the following claims.

We claim:
 1. A method of characterizing blood or blood product,comprising: a) providing a blood or blood product sample from a subject;b) assaying said sample to detect the presence of epithelialcell-specific DNA; c) creating a record reporting the presence orabsence of epithelial cell-specific DNA in the blood or blood productfrom said subject, wherein the presence of epithelial cell-specific DNAis indicative of the presence of epithelial cells or epithelialcell-specific DNA in said blood or blood product sample.
 2. The methodof claim 1, wherein said epithelial cell-specific DNA comprises a DNAthat is methylated in epithelial cells and is not methylated in bloodcells, and wherein the method comprises treating DNA from said samplewith a bisulfite reagent to create bisulfite-converted epithelialcell-specific DNA.
 3. The method of claim 2, wherein said epithelialcell-specific DNA comprises ZDHHC1 DNA.
 4. The method of claim 3,wherein said bisulfite-converted epithelial cell-specific DNA comprisesa DNA strand comprising the nucleotide sequence of SEQ ID NO:33.
 5. Amethod for monitoring a disease state in a subject, the methodcomprising the steps of: a) obtaining a first blood product sample fromthe subject at a first time point; b) initiating a treatment protocol,where said treatment protocol comprises therapeutic intervention; c)obtaining a second blood product sample from the subject at a secondtime point, wherein said second time point is after initiation of saidtreatment protocol; and d) assaying said first blood product sample andsaid second blood product sample for an amount of an epithelialcell-specific DNA, and e) generating a patient record reporting adifference in the amount of epithelial cell-specific DNA between saidfirst blood product sample and said second blood product, wherein adifference in the amount of epithelial cell-specific DNA between saidfirst blood product sample and said second blood product sample isindicative of a change in the disease state in said subject.
 6. Themethod of claim 5, wherein said treatment protocol comprises one or moreof surgery, drug therapy, chemotherapy, immunotherapy, nutritionaltherapy, radiation therapy, temperature therapy, and physical therapy.7. The method of claim 5, wherein a difference in the amount ofepithelial cell-specific DNA between said first blood product sample andsaid second blood product sample is indicative of recurrence,progression, or regression of the disease state in said subject.
 8. Themethod of claim 5, wherein said disease state is cancer.
 9. The methodof claim 8, wherein said cancer is metastatic cancer.
 10. The method ofclaim 5, wherein said blood product is plasma.
 11. A composition,comprising: a complex of a ZDHHC1 nucleic acid and at least oneoligonucleotide, wherein at least a portion of said oligonucleotide ishybridized to said ZDHHC1 nucleic acid.
 12. The composition of claim 54,wherein said ZDHHC1 nucleic acid is bisulfite-converted ZDHHC1 nucleicacid.
 13. A composition comprising a strand of DNA comprising thenucleotide sequence of SEQ ID NO:33 or comprising the nucleotidesequence of SEQ ID NO:27.
 14. The composition of claim 13, furthercomprising a detection probe oligonucleotide, wherein the detectionprobe oligonucleotide comprises a region that is complementary to aportion of said strand of DNA.
 15. The composition of claim 14, whereinthe detection probe oligonucleotide comprises a region that iscomplementary to a portion of SEQ ID NO:27.
 16. The composition of claim15, wherein said detection probe oligonucleotide comprises a reportermolecule.
 17. The composition of claim 16, where said reporter moleculecomprises a fluorophore.
 18. The composition of claim 14, wherein saiddetection probe oligonucleotide comprises a flap sequence.
 19. Thecomposition of claim 14, further comprising a FRET cassette.
 20. Thecomposition of claim 18, further comprising a FEN-1 endonuclease. 21.The composition of claim 14, further comprising a thermostable DNApolymerase.
 22. A reaction mixture comprising the composition of claim13.
 23. The reaction mixture of claim 22, further comprising one or moreof a primer, reporter oligonucleotide, a thermostable DNA polymerase, aFEN-1 endonuclease, and a FRET cassette.
 24. A kit, comprising: a) atleast one oligonucleotide, wherein at least a portion of saidoligonucleotide specifically hybridizes to bisulfite-converted ZDHHC1DNA; and b) bisulfite reagent.
 25. The kit of claim 24, comprising atleast one oligonucleotide that comprises a region that is complementaryto a portion of SEQ ID NO:27.
 26. The kit of claim 24, wherein saidoligonucleotide is selected from one or more of a captureoligonucleotide, a pair of nucleic acid primers, a nucleic acid probe,and an invasive oligonucleotide.
 27. A method of producing an amplifiedproduct, the method comprising: a) treating DNA from a blood or bloodproduct sample with a bisulfite reagent to produce bisulfite-convertedDNA; b) amplifying a region of said bisulfite-converted DNA using a pairof primers, wherein said amplifying produces amplified product having asequence comprising a region of SEQ ID NO:27.
 28. The method of claim27, further comprising a step of detecting the amplified product with adetection probe.
 29. The method of claim 28, wherein said detectionprobe comprises a reporter molecule.
 30. The method of claim 28, whereinsaid detection probe comprises a flap sequence.